33 CFR 165.504 - Newport News Shipbuilding and Dry Dock Company Shipyard, James River, Newport News, Va.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Newport News Shipbuilding and Dry Dock Company Shipyard, James River, Newport News, Va. 165.504 Section 165.504 Navigation and Navigable... Coast Guard District § 165.504 Newport News Shipbuilding and Dry Dock Company Shipyard, James River...

33 CFR 165.504 - Newport News Shipbuilding and Dry Dock Company Shipyard, James River, Newport News, Va.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Newport News Shipbuilding and Dry Dock Company Shipyard, James River, Newport News, Va. 165.504 Section 165.504 Navigation and Navigable... Coast Guard District § 165.504 Newport News Shipbuilding and Dry Dock Company Shipyard, James River...

33 CFR 165.504 - Newport News Shipbuilding and Dry Dock Company Shipyard, James River, Newport News, Va.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Newport News Shipbuilding and Dry Dock Company Shipyard, James River, Newport News, Va. 165.504 Section 165.504 Navigation and Navigable... Coast Guard District § 165.504 Newport News Shipbuilding and Dry Dock Company Shipyard, James River...

33 CFR 165.504 - Newport News Shipbuilding and Dry Dock Company Shipyard, James River, Newport News, Va.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Newport News Shipbuilding and Dry Dock Company Shipyard, James River, Newport News, Va. 165.504 Section 165.504 Navigation and Navigable... Coast Guard District § 165.504 Newport News Shipbuilding and Dry Dock Company Shipyard, James River...

33 CFR 165.504 - Newport News Shipbuilding and Dry Dock Company Shipyard, James River, Newport News, Va.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Newport News Shipbuilding and Dry Dock Company Shipyard, James River, Newport News, Va. 165.504 Section 165.504 Navigation and Navigable... Coast Guard District § 165.504 Newport News Shipbuilding and Dry Dock Company Shipyard, James River...

7. View from gate spanning mouth of Dry Dock 5, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

7. View from gate spanning mouth of Dry Dock 5, showing (1-r) north wall of Pier 10 and south wall of Pier 11. - Charlestown Navy Yard, Pier 10, Between Piers 9 & 11 along Mystic River on Charlestown Waterfront at eastern edge of Charlestown Navy Yard, Boston, Suffolk County, MA

38. Y&D Drawing 216455 (1942), 'Dry Dock 4 General Arrangement ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

38. Y&D Drawing 216455 (1942), 'Dry Dock 4 General Arrangement Sections F-F, G-G, H-H, I-I'; sectional views through pump room, flooding and dewatering chambers. - Hunters Point Naval Shipyard, Drydock No. 4, East terminus of Palou Avenue, San Francisco, San Francisco County, CA

37. PWD Drawing 11,654M35 (1987), 'Dry Dock No. 4 Utility ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

37. PWD Drawing 11,654-M-35 (1987), 'Dry Dock No. 4 Utility Low Pressure Sensors-Hunters Point'; showing basic plan view at upper level of pump room. - Hunters Point Naval Shipyard, Drydock No. 4, East terminus of Palou Avenue, San Francisco, San Francisco County, CA

33 CFR 110.190 - Tortugas Harbor, in vicinity of Garden Key, Dry Tortugas, Fla.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Garden Key, Dry Tortugas, Fla. 110.190 Section 110.190 Navigation and Navigable Waters COAST GUARD..., in vicinity of Garden Key, Dry Tortugas, Fla. (a) The anchorage grounds. All of Bird Key Harbor, southwest of Garden Key, bounded by the surrounding reefs and shoals and, on the northeast, by a line...

33 CFR 110.190 - Tortugas Harbor, in vicinity of Garden Key, Dry Tortugas, Fla.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Garden Key, Dry Tortugas, Fla. 110.190 Section 110.190 Navigation and Navigable Waters COAST GUARD..., in vicinity of Garden Key, Dry Tortugas, Fla. (a) The anchorage grounds. All of Bird Key Harbor, southwest of Garden Key, bounded by the surrounding reefs and shoals and, on the northeast, by a line...

33 CFR 110.190 - Tortugas Harbor, in vicinity of Garden Key, Dry Tortugas, Fla.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Garden Key, Dry Tortugas, Fla. 110.190 Section 110.190 Navigation and Navigable Waters COAST GUARD..., in vicinity of Garden Key, Dry Tortugas, Fla. (a) The anchorage grounds. All of Bird Key Harbor, southwest of Garden Key, bounded by the surrounding reefs and shoals and, on the northeast, by a line...

33 CFR 110.190 - Tortugas Harbor, in vicinity of Garden Key, Dry Tortugas, Fla.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Garden Key, Dry Tortugas, Fla. 110.190 Section 110.190 Navigation and Navigable Waters COAST GUARD..., in vicinity of Garden Key, Dry Tortugas, Fla. (a) The anchorage grounds. All of Bird Key Harbor, southwest of Garden Key, bounded by the surrounding reefs and shoals and, on the northeast, by a line...

33 CFR 110.190 - Tortugas Harbor, in vicinity of Garden Key, Dry Tortugas, Fla.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Garden Key, Dry Tortugas, Fla. 110.190 Section 110.190 Navigation and Navigable Waters COAST GUARD..., in vicinity of Garden Key, Dry Tortugas, Fla. (a) The anchorage grounds. All of Bird Key Harbor, southwest of Garden Key, bounded by the surrounding reefs and shoals and, on the northeast, by a line...

6. Looking west showing top of dock: steaming frozen ore ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

6. Looking west showing top of dock: steaming frozen ore which had been put in pockets in December 1959, May 6, 1990. Photographer: unknown - Marquette Ore Dock No. 6, Ore Dock, On pilings in Marquette City Lower Harbor, Marquette, Marquette County, MI

18 CFR 1304.404 - Commercial marina harbor limits.

Code of Federal Regulations, 2010 CFR

2010-04-01

... facilities at the dock, navigation and flood control requirements, optimum use of lands and land rights owned... to, changes in the ownership of the land base supporting the marina. ... harbor areas are determined by the extent of land rights held by the dock operator. The lakeward limits...

29 CFR 1915.75 - Access to and guarding of dry docks and marine railways.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 29 Labor 7 2010-07-01 2010-07-01 false Access to and guarding of dry docks and marine railways... railways. The provisions of this section shall apply to ship repairing, shipbuilding and shipbreaking. (a... applicable requirements of § 1915.72. (g) Catwalks on stiles of marine railways shall be no less than 20...

33 CFR 110.83 - Chicago Harbor, Ill.

Code of Federal Regulations, 2013 CFR

2013-07-01

... South of the South face of the former Naval Armory Dock, and 100 feet East of said bulkhead, that point... parallel to the aforesaid harbor line and is approximately 800 feet South of the South face of the former Naval Armory Dock, said point is 20 feet East of the East face of the Chicago Park District jetty...

33 CFR 401.65 - Communication-ports, docks and anchorages.

Code of Federal Regulations, 2010 CFR

2010-07-01

... anchorages. 401.65 Section 401.65 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT....65 Communication—ports, docks and anchorages. (a) Every vessel entering or leaving a lake port shall... the harbor entrance. (b) Every vessel arriving at a port, dock or anchorage shall report to the...

33 CFR 401.65 - Communication-ports, docks and anchorages.

Code of Federal Regulations, 2014 CFR

2014-07-01

... anchorages. 401.65 Section 401.65 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT....65 Communication—ports, docks and anchorages. (a) Every vessel entering or leaving a lake port shall... the harbor entrance. (b) Every vessel arriving at a port, dock or anchorage shall report to the...

33 CFR 401.65 - Communication-ports, docks and anchorages.

Code of Federal Regulations, 2011 CFR

2011-07-01

... anchorages. 401.65 Section 401.65 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT....65 Communication—ports, docks and anchorages. (a) Every vessel entering or leaving a lake port shall... the harbor entrance. (b) Every vessel arriving at a port, dock or anchorage shall report to the...

33 CFR 401.65 - Communication-ports, docks and anchorages.

Code of Federal Regulations, 2013 CFR

2013-07-01

... anchorages. 401.65 Section 401.65 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT....65 Communication—ports, docks and anchorages. (a) Every vessel entering or leaving a lake port shall... the harbor entrance. (b) Every vessel arriving at a port, dock or anchorage shall report to the...

33 CFR 401.65 - Communication-ports, docks and anchorages.

Code of Federal Regulations, 2012 CFR

2012-07-01

... anchorages. 401.65 Section 401.65 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT....65 Communication—ports, docks and anchorages. (a) Every vessel entering or leaving a lake port shall... the harbor entrance. (b) Every vessel arriving at a port, dock or anchorage shall report to the...

Annual Report: 2011-2012 Storm Season Sampling, Non-Dry Dock Stormwater Monitoring for Puget Sound Naval Shipyard, Bremerton, WA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandenberger, Jill M.; Metallo, David; Rupert, Brian

2013-07-03

Annual PSNS non-dry dock storm water monitoring results for 2011-2012 storm season. Included are a brief description of the sampling procedures, storm event information, laboratory methods and data collection, a results and discussion section, and the conclusions and recommendations.

Overview of Shipyard coast line with Piers G1, G2, G3, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Overview of Shipyard coast line with Piers G-1, G-2, G-3, G-4, and G-5 in view, view facing east-southeast - U.S. Naval Base, Pearl Harbor, Pier & Quay Walls, Entrance to Dry Dock No. 2 & Repair Wharfs, east & west sides of Dry Dock No. 2 & west side of Dry Dock No. 3, Pearl City, Honolulu County, HI

View of southeast side, faint "141" sign, Cranes P76 and ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

View of southeast side, faint "141" sign, Cranes P-76 and P-71 are behind, view facing northwest - U.S. Naval Base, Pearl Harbor, Dry Dock No. 1, Latrine, Sixth Street, adjacent to Dry Dock No. 1, Pearl City, Honolulu County, HI

Photocopy. U.S. Navy photograph, 1945. Dock and service area of ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Photocopy. U.S. Navy photograph, 1945. Dock and service area of Waipio Peninsula Amphibious Base (BMA - CP 121, 958) - U.S. Naval Base, Pearl Harbor, Waipio Peninsula, Waipo Peninsula, Pearl City, Honolulu County, HI

View of south end with two entry doors, signs say ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

View of south end with two entry doors, signs say "Men" and "No Smoking" (two times), view facing north-northeast - U.S. Naval Base, Pearl Harbor, Dry Dock No. 1, Latrine, Sixth Street, adjacent to Dry Dock No. 1, Pearl City, Honolulu County, HI

Interior of east side bathroom showing the sloped ceiling and ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Interior of east side bathroom showing the sloped ceiling and window grill openings, light coming from right to left, view facing north-northeast - U.S. Naval Base, Pearl Harbor, Dry Dock No. 1, Latrine, Sixth Street, adjacent to Dry Dock No. 1, Pearl City, Honolulu County, HI

UT088 ATV docking_239C

NASA Image and Video Library

2012-03-28

ISS030-E-175366 (28 March 2012) --- European Space Agency?s ?Edoardo Amaldi? Automated Transfer Vehicle-3 (ATV-3) docks with the International Space Station, delivering 220 pounds of oxygen, 628 pounds of water, 4.5 tons of propellant, and nearly 2.5 tons of dry cargo, including experiment hardware, spare parts, food and clothing. Docking of the two spacecraft occurred at 6:31 p.m. (EDT) on March 28, 2012.

Annual Report: 2010-2011 Storm Season Sampling For NON-DRY DOCK STORMWATER MONITORING FOR PUGET SOUND NAVAL SHIPYARD, BREMERTON, WA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandenberger, Jill M.; Metallo, David; Johnston, Robert K.

2012-09-01

This interim report summarizes the stormwater monitoring conducted for non-dry dock outfalls in both the confined industrial area and the residential areas of Naval Base Kitsap within the Puget Sound Naval Shipyard (referred to as the Shipyard). This includes the collection, analyses, and descriptive statistics for stormwater sampling conducted from November 2010 through April 2011. Seven stormwater basins within the Shipyard were sampled during at least three storm events to characterize non-dry dock stormwater discharges at selected stormwater drains located within the facility. This serves as the Phase I component of the project and Phase II is planned for themore » 2011-2012 storm season. These data will assist the Navy, USEPA, Ecology and other stakeholders in understanding the nature and condition of stormwater discharges from the Shipyard and inform the permitting process for new outfall discharges. The data from Phase I was compiled with current stormwater data available from the Shipyard, Sinclair/Dyes Inlet watershed, and Puget Sound in order to support technical investigations for the Draft NPDES permit. The permit would require storm event sampling at selected stormwater drains located within the Shipyard. However, the data must be considered on multiple scales to truly understand potential impairments to beneficial uses within Sinclair and Dyes Inlets.« less

PharmDock: a pharmacophore-based docking program

PubMed Central

2014-01-01

Background Protein-based pharmacophore models are enriched with the information of potential interactions between ligands and the protein target. We have shown in a previous study that protein-based pharmacophore models can be applied for ligand pose prediction and pose ranking. In this publication, we present a new pharmacophore-based docking program PharmDock that combines pose sampling and ranking based on optimized protein-based pharmacophore models with local optimization using an empirical scoring function. Results Tests of PharmDock on ligand pose prediction, binding affinity estimation, compound ranking and virtual screening yielded comparable or better performance to existing and widely used docking programs. The docking program comes with an easy-to-use GUI within PyMOL. Two features have been incorporated in the program suite that allow for user-defined guidance of the docking process based on previous experimental data. Docking with those features demonstrated superior performance compared to unbiased docking. Conclusion A protein pharmacophore-based docking program, PharmDock, has been made available with a PyMOL plugin. PharmDock and the PyMOL plugin are freely available from http://people.pharmacy.purdue.edu/~mlill/software/pharmdock. PMID:24739488

Waterborne Commerce of the United States Calendar Year 1987. Part 3. Waterways and Harbors Great Lakes

DTIC Science & Technology

1989-05-31

0-;......... .......... ALPENA HARBOR, MICH. SE CTION INCLUDEDl6. j LOWE 4,00 FET OF RIVER ANDPRIVATE HARORS NORTH IF MOUTH OF THUNDER...1,821,� 1967..................................................... 1,968,6s DETROIT, hMI, DISTRICT 31 ALPENA HARBOR, MICH...TANKER N050RG TANKER OR DRY CARGO TANKER DRY CARGO TUGBOAT DRY CARGO TUGBOATIO ALPENA HARGORP MICH. I BON OUTIOUND 22 . . . . . . . . . . . . . . 2 34

F2Dock: Fast Fourier Protein-Protein Docking

PubMed Central

Bajaj, Chandrajit; Chowdhury, Rezaul; Siddavanahalli, Vinay

2009-01-01

The functions of proteins is often realized through their mutual interactions. Determining a relative transformation for a pair of proteins and their conformations which form a stable complex, reproducible in nature, is known as docking. It is an important step in drug design, structure determination and understanding function and structure relationships. In this paper we extend our non-uniform fast Fourier transform docking algorithm to include an adaptive search phase (both translational and rotational) and thereby speed up its execution. We have also implemented a multithreaded version of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code F2Dock (F2 = Fast Fourier). We have calibrated F2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that F2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic potential based scores only, F2Dock is structured to incorporate Lennard-Jones potential and re-ranking docking solutions based on desolvation energy. PMID:21071796

Submarine harbor navigation using image data

NASA Astrophysics Data System (ADS)

Stubberud, Stephen C.; Kramer, Kathleen A.

2017-01-01

The process of ingress and egress of a United States Navy submarine is a human-intensive process that takes numerous individuals to monitor locations and for hazards. Sailors pass vocal information to bridge where it is processed manually. There is interest in using video imaging of the periscope view to more automatically provide navigation within harbors and other points of ingress and egress. In this paper, video-based navigation is examined as a target-tracking problem. While some image-processing methods claim to provide range information, the moving platform problem and weather concerns, such as fog, reduce the effectiveness of these range estimates. The video-navigation problem then becomes an angle-only tracking problem. Angle-only tracking is known to be fraught with difficulties, due to the fact that the unobservable space is not the null space. When using a Kalman filter estimator to perform the tracking, significant errors arise which could endanger the submarine. This work analyzes the performance of the Kalman filter when angle-only measurements are used to provide the target tracks. This paper addresses estimation unobservability and the minimal set of requirements that are needed to address it in this complex but real-world problem. Three major issues are addressed: the knowledge of navigation beacons/landmarks' locations, the minimal number of these beacons needed to maintain the course, and update rates of the angles of the landmarks as the periscope rotates and landmarks become obscured due to blockage and weather. The goal is to address the problem of navigation to and from the docks, while maintaining the traversing of the harbor channel based on maritime rules relying solely on the image-based data. The minimal number of beacons will be considered. For this effort, the image correlation from frame to frame is assumed to be achieved perfectly. Variation in the update rates and the dropping of data due to rotation and obscuration is considered

Molecular docking.

PubMed

Morris, Garrett M; Lim-Wilby, Marguerita

2008-01-01

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.

A Probabilistic and Observation Based Methodology to Estimate Small Craft Harbor Vulnerability to Tsunami Events

NASA Astrophysics Data System (ADS)

Keen, A. S.; Lynett, P. J.; Ayca, A.

2016-12-01

Because of the damage resulting from the 2010 Chile and 2011 Japanese tele-tsunamis, the tsunami risk to the small craft marinas in California has become an important concern. The talk will outline an assessment tool which can be used to assess the tsunami hazard to small craft harbors. The methodology is based on the demand and structural capacity of the floating dock system, composed of floating docks/fingers and moored vessels. The structural demand is determined using a Monte Carlo methodology. Monte Carlo methodology is a probabilistic computational tool where the governing might be well known, but the independent variables of the input (demand) as well as the resisting structural components (capacity) may not be completely known. The Monte Carlo approach uses a distribution of each variable, and then uses that random variable within the described parameters, to generate a single computation. The process then repeats hundreds or thousands of times. The numerical model "Method of Splitting Tsunamis" (MOST) has been used to determine the inputs for the small craft harbors within California. Hydrodynamic model results of current speed, direction and surface elevation were incorporated via the drag equations to provide the bases of the demand term. To determine the capacities, an inspection program was developed to identify common features of structural components. A total of six harbors have been inspected ranging from Crescent City in Northern California to Oceanside Harbor in Southern California. Results from the inspection program were used to develop component capacity tables which incorporated the basic specifications of each component (e.g. bolt size and configuration) and a reduction factor (which accounts for the component reduction in capacity with age) to estimate in situ capacities. Like the demand term, these capacities are added probabilistically into the model. To date the model has been applied to Santa Cruz Harbor as well as Noyo River. Once

Design for navigation improvements at Nome Harbor, Alaska: Coastal model investigation. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bottin, R.R.; Acuff, H.F.

1998-09-01

A 1:90-scale (undistorted) three dimensional coastal hydraulic model was used to investigate the design of proposed navigation improvements at Nome Harbor, Alaska, with respect to wave, current, and shoaling conditions at the site. The model reproduced about 3,350 m (11,000 ft) of the Alaskan shoreline, the existing harbor and lower reaches of the Snake River, and sufficient offshore bathymetry in the Norton Sound to permit generation of the required experimental waves. The model was used to determine the impacts of a new entrance channel on wave-induced current patterns and magnitudes, sediment transport patterns, and wave conditions in the new channelmore » and harbor area, as well as to optimize the lengths and alignments of new breakwaters and causeway extensions. A 24.4-m-long (9O-ft-long) unidirectional, spectral wave generator, and automated data acquisition and control system, and a crushed coal tracer material were utilized in model operation. It was concluded from study results that: (a) existing conditions are characterized by rough and turbulent wave conditions in the existing entrance. Very confused wave patterns were observed in the entrance due to wave energy reflected off the vertical walls lining the entrance. Wave heights in excess of 1.5 m (5 ft) were obtained in the entrance for typical storm conditions; and wave heights of almost 3.7 m (12 ft) were obtained in the entrance for 5O-year storm wave conditions with extreme high-water level 4 m (+13 ft); (b) wave conditions along the vertical-faced causeway docks were excessive for existing conditions. Wave heights in excess of 3.7 and 2.7 m (12 and 9 ft) were obtained along the outer and inner docks, respectively, for typical storm conditions; and wave heights of almost 7 and 5.8 m (23 and 19 ft) were recorded along these docks, respectively, for 5-year storm wave conditions with extreme high-water levels.« less

DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina.

PubMed

Di Muzio, Elena; Toti, Daniele; Polticelli, Fabio

2017-02-01

Molecular docking is a powerful technique that helps uncover the structural and energetic bases of the interaction between macromolecules and substrates, endogenous and exogenous ligands, and inhibitors. Moreover, this technique plays a pivotal role in accelerating the screening of large libraries of compounds for drug development purposes. The need to promote community-driven drug development efforts, especially as far as neglected diseases are concerned, calls for user-friendly tools to allow non-expert users to exploit the full potential of molecular docking. Along this path, here is described the implementation of DockingApp, a freely available, extremely user-friendly, platform-independent application for performing docking simulations and virtual screening tasks using AutoDock Vina. DockingApp sports an intuitive graphical user interface which greatly facilitates both the input phase and the analysis of the results, which can be visualized in graphical form using the embedded JMol applet. The application comes with the DrugBank set of more than 1400 ready-to-dock, FDA-approved drugs, to facilitate virtual screening and drug repurposing initiatives. Furthermore, other databases of compounds such as ZINC, available also in AutoDock format, can be readily and easily plugged in.

DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina

NASA Astrophysics Data System (ADS)

Di Muzio, Elena; Toti, Daniele; Polticelli, Fabio

2017-02-01

Molecular docking is a powerful technique that helps uncover the structural and energetic bases of the interaction between macromolecules and substrates, endogenous and exogenous ligands, and inhibitors. Moreover, this technique plays a pivotal role in accelerating the screening of large libraries of compounds for drug development purposes. The need to promote community-driven drug development efforts, especially as far as neglected diseases are concerned, calls for user-friendly tools to allow non-expert users to exploit the full potential of molecular docking. Along this path, here is described the implementation of DockingApp, a freely available, extremely user-friendly, platform-independent application for performing docking simulations and virtual screening tasks using AutoDock Vina. DockingApp sports an intuitive graphical user interface which greatly facilitates both the input phase and the analysis of the results, which can be visualized in graphical form using the embedded JMol applet. The application comes with the DrugBank set of more than 1400 ready-to-dock, FDA-approved drugs, to facilitate virtual screening and drug repurposing initiatives. Furthermore, other databases of compounds such as ZINC, available also in AutoDock format, can be readily and easily plugged in.

Magnetic docking aid for orbiter to ISS docking

NASA Technical Reports Server (NTRS)

Schneider, William C.; Nagy, Kornel; Schliesing, John A.

1996-01-01

The present docking system for the Orbiter uses mechanical capture latches that are actuated by contact forces. The forces are generated when the two approaching masses collide at the docking mechanism. There is always a trade-off between having high enough momentum to effect capture and low enough momentum to avoid structural overload or unacceptable angular displacements. The use of the present docking system includes a contact thrusting maneuver that causes high docking loads to be included into Space Station. A magnetic docking aid has been developed to reduce the load s during docking. The magnetic docking aid is comprised of two extendible booms that are attached adjacent to the docking structure with electromagnets attached on the end of the boom. On the mating vehicle, two steel plates are attached. As the Orbiter approaches Space Station, the booms are extended, and the magnets attach to the actuated (without thrusting), by slowly driving the extendible booms to the stowed position, thus reacting the load into the booms. This results in a docking event that has lower loads induced into Space Station structure. This method also greatly simplifies the Station berthing tasks, since the Shuttle Remote Manipulation System (SRMS) arm need only place the element to be berthed on the magnets (no load required), rather than firing the Reaction Control System (RCS) jets to provide the required force for capture latch actuation. The Magnetic Docking Aid was development testing on a six degree-of-freedom (6 DOF) system at JSC.

5. Aerial view (altitude 5,000 ft.) looking southeast showing Dry ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

5. Aerial view (altitude 5,000 ft.) looking southeast showing Dry Dock No. 4. completed (top center). Note major expansion of land mass to south of Dry Dock No. 4 resulting from placement of excavated soils and rock prior to and during construction (8/3/43). Photographer: Mr. Rudnick, PHoM 2/C. - Hunters Point Naval Shipyard, Drydock No. 4, East terminus of Palou Avenue, San Francisco, San Francisco County, CA

AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking.

PubMed

Ben-Shimon, Avraham; Niv, Masha Y

2015-05-05

The huge conformational space stemming from the inherent flexibility of peptides is among the main obstacles to successful and efficient computational modeling of protein-peptide interactions. Current peptide docking methods typically overcome this challenge using prior knowledge from the structure of the complex. Here we introduce AnchorDock, a peptide docking approach, which automatically targets the docking search to the most relevant parts of the conformational space. This is done by precomputing the free peptide's structure and by computationally identifying anchoring spots on the protein surface. Next, a free peptide conformation undergoes anchor-driven simulated annealing molecular dynamics simulations around the predicted anchoring spots. In the challenging task of a completely blind docking test, AnchorDock produced exceptionally good results (backbone root-mean-square deviation ≤ 2.2Å, rank ≤15) for 10 of 13 unbound cases tested. The impressive performance of AnchorDock supports a molecular recognition pathway that is driven via pre-existing local structural elements. Copyright © 2015 Elsevier Ltd. All rights reserved.

Surflex-Dock: Docking benchmarks and real-world application

NASA Astrophysics Data System (ADS)

Spitzer, Russell; Jain, Ajay N.

2012-06-01

Benchmarks for molecular docking have historically focused on re-docking the cognate ligand of a well-determined protein-ligand complex to measure geometric pose prediction accuracy, and measurement of virtual screening performance has been focused on increasingly large and diverse sets of target protein structures, cognate ligands, and various types of decoy sets. Here, pose prediction is reported on the Astex Diverse set of 85 protein ligand complexes, and virtual screening performance is reported on the DUD set of 40 protein targets. In both cases, prepared structures of targets and ligands were provided by symposium organizers. The re-prepared data sets yielded results not significantly different than previous reports of Surflex-Dock on the two benchmarks. Minor changes to protein coordinates resulting from complex pre-optimization had large effects on observed performance, highlighting the limitations of cognate ligand re-docking for pose prediction assessment. Docking protocols developed for cross-docking, which address protein flexibility and produce discrete families of predicted poses, produced substantially better performance for pose prediction. Performance on virtual screening performance was shown to benefit by employing and combining multiple screening methods: docking, 2D molecular similarity, and 3D molecular similarity. In addition, use of multiple protein conformations significantly improved screening enrichment.

A python-based docking program utilizing a receptor bound ligand shape: PythDock.

PubMed

Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi

2011-09-01

PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and docked pose, i.e., average root mean squared deviation values of the bound ligand were compared for fourteen protein-ligand complexes. Since the number of ligands' rotational flexibility is an important factor affecting the accuracy of a docking, the data set was chosen to have various degrees of flexibility. Although PythDock has a scoring function simpler than those of other programs (AutoDock and DOCK), our results showed that PythDock predicted more accurate poses than both AutoDock4.2 and DOCK6.2. This indicates that PythDock could be a useful tool to study ligand-receptor interactions and could also be beneficial in structure based drug design.

DockQ: A Quality Measure for Protein-Protein Docking Models

PubMed Central

Basu, Sankar

2016-01-01

The state-of-the-art to assess the structural quality of docking models is currently based on three related yet independent quality measures: Fnat, LRMS, and iRMS as proposed and standardized by CAPRI. These quality measures quantify different aspects of the quality of a particular docking model and need to be viewed together to reveal the true quality, e.g. a model with relatively poor LRMS (>10Å) might still qualify as 'acceptable' with a descent Fnat (>0.50) and iRMS (<3.0Å). This is also the reason why the so called CAPRI criteria for assessing the quality of docking models is defined by applying various ad-hoc cutoffs on these measures to classify a docking model into the four classes: Incorrect, Acceptable, Medium, or High quality. This classification has been useful in CAPRI, but since models are grouped in only four bins it is also rather limiting, making it difficult to rank models, correlate with scoring functions or use it as target function in machine learning algorithms. Here, we present DockQ, a continuous protein-protein docking model quality measure derived by combining Fnat, LRMS, and iRMS to a single score in the range [0, 1] that can be used to assess the quality of protein docking models. By using DockQ on CAPRI models it is possible to almost completely reproduce the original CAPRI classification into Incorrect, Acceptable, Medium and High quality. An average PPV of 94% at 90% Recall demonstrating that there is no need to apply predefined ad-hoc cutoffs to classify docking models. Since DockQ recapitulates the CAPRI classification almost perfectly, it can be viewed as a higher resolution version of the CAPRI classification, making it possible to estimate model quality in a more quantitative way using Z-scores or sum of top ranked models, which has been so valuable for the CASP community. The possibility to directly correlate a quality measure to a scoring function has been crucial for the development of scoring functions for protein structure

GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing.

PubMed

Kantardjiev, Alexander A

2011-07-01

GPU.proton.DOCK (Genuine Protein Ultrafast proton equilibria consistent DOCKing) is a state of the art service for in silico prediction of protein-protein interactions via rigorous and ultrafast docking code. It is unique in providing stringent account of electrostatic interactions self-consistency and proton equilibria mutual effects of docking partners. GPU.proton.DOCK is the first server offering such a crucial supplement to protein docking algorithms--a step toward more reliable and high accuracy docking results. The code (especially the Fast Fourier Transform bottleneck and electrostatic fields computation) is parallelized to run on a GPU supercomputer. The high performance will be of use for large-scale structural bioinformatics and systems biology projects, thus bridging physics of the interactions with analysis of molecular networks. We propose workflows for exploring in silico charge mutagenesis effects. Special emphasis is given to the interface-intuitive and user-friendly. The input is comprised of the atomic coordinate files in PDB format. The advanced user is provided with a special input section for addition of non-polypeptide charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. The output is comprised of docked complexes in PDB format as well as interactive visualization in a molecular viewer. GPU.proton.DOCK server can be accessed at http://gpudock.orgchm.bas.bg/.

VIEW OF FACILITY NO. S 20 SHOWING THE EXTANT NARROWGAUGE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

VIEW OF FACILITY NO. S 20 SHOWING THE EXTANT NARROW-GAUGE TRACKS AND ASPHALT-FILLED TRACKWAY. VIEW FACING SOUTHWEST - U.S. Naval Base, Pearl Harbor, Floating Dry Dock Quay, Hurt Avenue at northwest side of Magazine Loch, Pearl City, Honolulu County, HI

SAMPL4 & DOCK3.7: lessons for automated docking procedures

NASA Astrophysics Data System (ADS)

Coleman, Ryan G.; Sterling, Teague; Weiss, Dahlia R.

2014-03-01

The SAMPL4 challenges were used to test current automated methods for solvation energy, virtual screening, pose and affinity prediction of the molecular docking pipeline DOCK 3.7. Additionally, first-order models of binding affinity were proposed as milestones for any method predicting binding affinity. Several important discoveries about the molecular docking software were made during the challenge: (1) Solvation energies of ligands were five-fold worse than any other method used in SAMPL4, including methods that were similarly fast, (2) HIV Integrase is a challenging target, but automated docking on the correct allosteric site performed well in terms of virtual screening and pose prediction (compared to other methods) but affinity prediction, as expected, was very poor, (3) Molecular docking grid sizes can be very important, serious errors were discovered with default settings that have been adjusted for all future work. Overall, lessons from SAMPL4 suggest many changes to molecular docking tools, not just DOCK 3.7, that could improve the state of the art. Future difficulties and projects will be discussed.

Validation studies of the site-directed docking program LibDock.

PubMed

Rao, Shashidhar N; Head, Martha S; Kulkarni, Amit; LaLonde, Judith M

2007-01-01

The performance of the site-features docking algorithm LibDock has been evaluated across eight GlaxoSmithKline targets as a follow-up to a broad validation study of docking and scoring software (Warren, G. L.; Andrews, W. C.; Capelli, A.; Clarke, B.; Lalonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Walls, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. J. Med. Chem. 2006, 49, 5912-5931). Docking experiments were performed to assess both the accuracy in reproducing the binding mode of the ligand and the retrieval of active compounds in a virtual screening protocol using both the DJD (Diller, D. J.; Merz, K. M., Jr. Proteins 2001, 43, 113-124) and LigScore2 (Krammer, A. K.; Kirchoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. J. Mol. Graphics Modell. 2005, 23, 395-407) scoring functions. This study was conducted using DJD scoring, and poses were rescored using all available scoring functions in the Accelrys LigandFit module, including LigScore2. For six out of eight targets at least 30% of the ligands were docked within a root-mean-square difference (RMSD) of 2.0 A for the crystallographic poses when the LigScore2 scoring function was used. LibDock retrieved at least 20% of active compounds in the top 10% of screened ligands for four of the eight targets in the virtual screening protocol. In both studies the LigScore2 scoring function enhanced the retrieval of crystallographic poses or active compounds in comparison with the results obtained using the DJD scoring function. The results for LibDock accuracy and ligand retrieval in virtual screening are compared to 10 other docking and scoring programs. These studies demonstrate the utility of the LigScore2 scoring function and that LibDock as a feature directed docking method performs as well as docking programs that use genetic/growing and Monte Carlo driven algorithms.

Replica Exchange Improves Sampling in Low-Resolution Docking Stage of RosettaDock

PubMed Central

Zhang, Zhe; Lange, Oliver F.

2013-01-01

Many protein-protein docking protocols are based on a shotgun approach, in which thousands of independent random-start trajectories minimize the rigid-body degrees of freedom. Another strategy is enumerative sampling as used in ZDOCK. Here, we introduce an alternative strategy, ReplicaDock, using a small number of long trajectories of temperature replica exchange. We compare replica exchange sampling as low-resolution stage of RosettaDock with RosettaDock's original shotgun sampling as well as with ZDOCK. A benchmark of 30 complexes starting from structures of the unbound binding partners shows improved performance for ReplicaDock and ZDOCK when compared to shotgun sampling at equal or less computational expense. ReplicaDock and ZDOCK consistently reach lower energies and generate significantly more near-native conformations than shotgun sampling. Accordingly, they both improve typical metrics of prediction quality of complex structures after refinement. Additionally, the refined ReplicaDock ensembles reach significantly lower interface energies and many previously hidden features of the docking energy landscape become visible when ReplicaDock is applied. PMID:24009670

Intuitive, but not simple: including explicit water molecules in protein-protein docking simulations improves model quality.

PubMed

Parikh, Hardik I; Kellogg, Glen E

2014-06-01

Characterizing the nature of interaction between proteins that have not been experimentally cocrystallized requires a computational docking approach that can successfully predict the spatial conformation adopted in the complex. In this work, the Hydropathic INTeractions (HINT) force field model was used for scoring docked models in a data set of 30 high-resolution crystallographically characterized "dry" protein-protein complexes and was shown to reliably identify native-like models. However, most current protein-protein docking algorithms fail to explicitly account for water molecules involved in bridging interactions that mediate and stabilize the association of the protein partners, so we used HINT to illuminate the physical and chemical properties of bridging waters and account for their energetic stabilizing contributions. The HINT water Relevance metric identified the "truly" bridging waters at the 30 protein-protein interfaces and we utilized them in "solvated" docking by manually inserting them into the input files for the rigid body ZDOCK program. By accounting for these interfacial waters, a statistically significant improvement of ∼24% in the average hit-count within the top-10 predictions the protein-protein dataset was seen, compared to standard "dry" docking. The results also show scoring improvement, with medium and high accuracy models ranking much better than incorrect ones. These improvements can be attributed to the physical presence of water molecules that alter surface properties and better represent native shape and hydropathic complementarity between interacting partners, with concomitantly more accurate native-like structure predictions. © 2013 Wiley Periodicals, Inc.

Protein-Protein Docking with F2Dock 2.0 and GB-Rerank

PubMed Central

Chowdhury, Rezaul; Rasheed, Muhibur; Keidel, Donald; Moussalem, Maysam; Olson, Arthur; Sanner, Michel; Bajaj, Chandrajit

2013-01-01

Motivation Computational simulation of protein-protein docking can expedite the process of molecular modeling and drug discovery. This paper reports on our new F2 Dock protocol which improves the state of the art in initial stage rigid body exhaustive docking search, scoring and ranking by introducing improvements in the shape-complementarity and electrostatics affinity functions, a new knowledge-based interface propensity term with FFT formulation, a set of novel knowledge-based filters and finally a solvation energy (GBSA) based reranking technique. Our algorithms are based on highly efficient data structures including the dynamic packing grids and octrees which significantly speed up the computations and also provide guaranteed bounds on approximation error. Results The improved affinity functions show superior performance compared to their traditional counterparts in finding correct docking poses at higher ranks. We found that the new filters and the GBSA based reranking individually and in combination significantly improve the accuracy of docking predictions with only minor increase in computation time. We compared F2 Dock 2.0 with ZDock 3.0.2 and found improvements over it, specifically among 176 complexes in ZLab Benchmark 4.0, F2 Dock 2.0 finds a near-native solution as the top prediction for 22 complexes; where ZDock 3.0.2 does so for 13 complexes. F2 Dock 2.0 finds a near-native solution within the top 1000 predictions for 106 complexes as opposed to 104 complexes for ZDock 3.0.2. However, there are 17 and 15 complexes where F2 Dock 2.0 finds a solution but ZDock 3.0.2 does not and vice versa; which indicates that the two docking protocols can also complement each other. Availability The docking protocol has been implemented as a server with a graphical client (TexMol) which allows the user to manage multiple docking jobs, and visualize the docked poses and interfaces. Both the server and client are available for download. Server: http

Docking system for spacecraft

NASA Technical Reports Server (NTRS)

Kahn, Jon B. (Inventor)

1988-01-01

A mechanism is disclosed for the docking of a spacecraft to a space station where a connection for transfer of personnel and equipment is desired. The invention comprises an active docking structure on a spacecraft and a passive docking structure on the station. The passive structure includes a docking ring mounted on a tunnel structure fixed to the space station. The active structure includes a docking ring carried by an actuator-attenuator devices, each attached at one end to the ring and at its other end in the spacecraft payload bay. The devices respond to command signals for moving the docking ring between a stowed position in the spacecraft to a deployed position suitable for engagement with the docking ring. The devices comprise means responsive to signals of sensed loadings to absorb impact energy and retraction means for drawing the coupled spacecraft and station into final docked configuration and moving the tunnel structure to a berthed position in the spacecraft. Latches couple the spacecraft and space station upon contact of the docking rings and latches establish a structural tie between the spacecraft when retracted.

GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking

NASA Astrophysics Data System (ADS)

Baek, Minkyung; Shin, Woong-Hee; Chung, Hwan Won; Seok, Chaok

2017-07-01

Protein-ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein-ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein-ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.

Docking system for spacecraft

NASA Technical Reports Server (NTRS)

Kahn, Jon B. (Inventor)

1990-01-01

A mechanism for the docking of a space vehicle to a space station where a connection for transfer of personnel and equipment is desired. The invention comprises an active docking structure on a space vehicle 10 and a passive docking structure on a station 11. The passive structure includes a docking ring 50 mounted on a tunnel structure 35 fixed to the space station. The active structure including a docking ring 18 carried by actuator-attenuator devices 20, each attached at one end to the ring 18 and at its other end in the vehicle's payload bay 12. The devices 20 respond to command signals for moving the docking ring 18 between a stowed position in the space vehicle to a deployed position suitable for engagement with the docking ring 50. The devices 20 comprise means responsive to signals of sensed loadings to absorb impact energy and retraction means for drawing the coupled space vehicle and station into final docked configuration and moving the tunnel structure to a berthed position in the space vehicle 10. Latches 60 couple the space vehicle and space station upon contact of docking rings 18 and 50 and latches 41-48 establish a structural tie between the spacecraft when retracted.

DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction

PubMed Central

Xue, Li C.; Jordan, Rafael A.; EL-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant

2015-01-01

Selecting near-native conformations from the immense number of conformations generated by docking programs remains a major challenge in molecular docking. We introduce DockRank, a novel approach to scoring docked conformations based on the degree to which the interface residues of the docked conformation match a set of predicted interface residues. Dock-Rank uses interface residues predicted by partner-specific sequence homology-based protein–protein interface predictor (PS-HomPPI), which predicts the interface residues of a query protein with a specific interaction partner. We compared the performance of DockRank with several state-of-the-art docking scoring functions using Success Rate (the percentage of cases that have at least one near-native conformation among the top m conformations) and Hit Rate (the percentage of near-native conformations that are included among the top m conformations). In cases where it is possible to obtain partner-specific (PS) interface predictions from PS-HomPPI, DockRank consistently outperforms both (i) ZRank and IRAD, two state-of-the-art energy-based scoring functions (improving Success Rate by up to 4-fold); and (ii) Variants of DockRank that use predicted interface residues obtained from several protein interface predictors that do not take into account the binding partner in making interface predictions (improving success rate by up to 39-fold). The latter result underscores the importance of using partner-specific interface residues in scoring docked conformations. We show that DockRank, when used to re-rank the conformations returned by ClusPro, improves upon the original ClusPro rankings in terms of both Success Rate and Hit Rate. DockRank is available as a server at http://einstein.cs.iastate.edu/DockRank/. PMID:23873600

DockRank: ranking docked conformations using partner-specific sequence homology-based protein interface prediction.

PubMed

Xue, Li C; Jordan, Rafael A; El-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant

2014-02-01

Selecting near-native conformations from the immense number of conformations generated by docking programs remains a major challenge in molecular docking. We introduce DockRank, a novel approach to scoring docked conformations based on the degree to which the interface residues of the docked conformation match a set of predicted interface residues. DockRank uses interface residues predicted by partner-specific sequence homology-based protein-protein interface predictor (PS-HomPPI), which predicts the interface residues of a query protein with a specific interaction partner. We compared the performance of DockRank with several state-of-the-art docking scoring functions using Success Rate (the percentage of cases that have at least one near-native conformation among the top m conformations) and Hit Rate (the percentage of near-native conformations that are included among the top m conformations). In cases where it is possible to obtain partner-specific (PS) interface predictions from PS-HomPPI, DockRank consistently outperforms both (i) ZRank and IRAD, two state-of-the-art energy-based scoring functions (improving Success Rate by up to 4-fold); and (ii) Variants of DockRank that use predicted interface residues obtained from several protein interface predictors that do not take into account the binding partner in making interface predictions (improving success rate by up to 39-fold). The latter result underscores the importance of using partner-specific interface residues in scoring docked conformations. We show that DockRank, when used to re-rank the conformations returned by ClusPro, improves upon the original ClusPro rankings in terms of both Success Rate and Hit Rate. DockRank is available as a server at http://einstein.cs.iastate.edu/DockRank/. Copyright © 2013 Wiley Periodicals, Inc.

Comparative evaluation of several docking tools for docking small molecule ligands to DC-SIGN.

PubMed

Jug, Gregor; Anderluh, Marko; Tomašič, Tihomir

2015-06-01

Five docking tools, namely AutoDock, FRED, CDOCKER, FlexX and GOLD, have been critically examined, with the aim of selecting those most appropriate for use as docking tools for docking molecules to the lectin dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN). This lectin has been selected for its rather non-druggable binding site, which enables complex interactions that guide the binding of the core monosaccharide. Since optimal orientation is crucial for forming coordination bonds, it was important to assess whether the selected docking tools could reproduce the optimal binding conformation for several oligosaccharides that are known to bind DC-SIGN. Our results show that even widely used docking programs have certain limitations when faced with a rather shallow and featureless binding site, as is the case of DC-SIGN. The FRED docking software (OpenEye Scientific Software, Inc.) was found to score as the best tool for docking ligands to DC-SIGN. The performance of FRED was further assessed on another lectin, Langerin. We have demonstrated that this validated docking protocol could be used for docking to other lectins similar to DC-SIGN.

4. Aerial view (altitude 2,000 ft.) looking north showing Dry ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. Aerial view (altitude 2,000 ft.) looking north showing Dry Dock No. 4 (upper left) under construction. Cofferdam is still in place. Note caisson sitting in caisson seat at east end of dock (2/8/43). Photographer: A. E. Weed, CPHoM. - Hunters Point Naval Shipyard, Drydock No. 4, East terminus of Palou Avenue, San Francisco, San Francisco County, CA

Microgravity experiments of nano-satellite docking mechanism for final rendezvous approach and docking phase

NASA Astrophysics Data System (ADS)

Ui, Kyoichi; Matunaga, Saburo; Satori, Shin; Ishikawa, Tomohiro

2005-09-01

Laboratory for Space Systems (LSS), Tokyo Institute of Technology (Tokyo Tech) conducted three-dimensional microgravity environment experiments about a docking mechanism for mothership-daughtership (MS-DS) nano-satellite using the facility of Japan Micro Gravity Center (JAMIC) with Hokkaido Institute of Technology (HIT). LSS has studied and developed a docking mechanism for MS-DS nano-satellite system in final rendezvous approach and docking phase since 2000. Consideration of the docking mechanism is to mate a nano-satellite stably while remaining control error of relative velocity and attitude because it is difficult for nano-satellite to have complicated attitude control and mating systems. Objective of the experiments is to verify fundamental grasping function based on our proposed docking methodology. The proposed docking sequence is divided between approach/grasping phase and guiding phase. In the approach/grasping phase, the docking mechanism grasps the nano-satellite even though the nano-satellite has relative position and attitude control errors as well as relative velocity in a docking space. In the guiding function, the docking mechanism guides the nano-satellite to a docking port while adjusting its attitude in order to transfer electrical power and fuel to the nano-satellite. In the paper, we describe the experimental system including the docking mechanism, control system, the daughtership system and the release mechanism, and describe results of microgravity experiments in JAMIC.

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

PubMed Central

Ravindranath, Pradeep Anand; Forli, Stefano; Goodsell, David S.; Olson, Arthur J.; Sanner, Michel F.

2015-01-01

Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approach include the: 1) exponential growth of the search space, demanding more efficient search methods; and 2) increased number of false positives, calling for scoring functions tailored for flexible receptor docking. We present AutoDockFR–AutoDock for Flexible Receptors (ADFR), a new docking engine based on the AutoDock4 scoring function, which addresses the aforementioned challenges with a new Genetic Algorithm (GA) and customized scoring function. We validate ADFR using the Astex Diverse Set, demonstrating an increase in efficiency and reliability of its GA over the one implemented in AutoDock4. We demonstrate greatly increased success rates when cross-docking ligands into apo receptors that require side-chain conformational changes for ligand binding. These cross-docking experiments are based on two datasets: 1) SEQ17 –a receptor diversity set containing 17 pairs of apo-holo structures; and 2) CDK2 –a ligand diversity set composed of one CDK2 apo structure and 52 known bound inhibitors. We show that, when cross-docking ligands into the apo conformation of the receptors with up to 14 flexible side-chains, ADFR reports more correctly cross-docked ligands than AutoDock Vina on both datasets with solutions found for 70.6% vs. 35.3% systems on SEQ17, and 76.9% vs. 61.5% on CDK2. ADFR also outperforms AutoDock Vina in number of top ranking solutions on both datasets. Furthermore, we show that correctly docked CDK2 complexes re-create on average 79.8% of all pairwise atomic interactions between the ligand and moving receptor atoms in the holo complexes. Finally, we show that

BP-Dock: A Flexible Docking Scheme for Exploring Protein–Ligand Interactions Based on Unbound Structures

PubMed Central

Bolia, Ashini; Gerek, Z. Nevin; Ozkan, S. Banu

2016-01-01

Molecular docking serves as an important tool in modeling protein–ligand interactions. However, it is still challenging to incorporate overall receptor flexibility, especially backbone flexibility, in docking due to the large conformational space that needs to be sampled. To overcome this problem, we developed a novel flexible docking approach, BP-Dock (Backbone Perturbation-Dock) that can integrate both backbone and side chain conformational changes induced by ligand binding through a multi-scale approach. In the BP-Dock method, we mimic the nature of binding-induced events as a first-order approximation by perturbing the residues along the protein chain with a small Brownian kick one at a time. The response fluctuation profile of the chain upon these perturbations is computed using the perturbation response scanning method. These response fluctuation profiles are then used to generate binding-induced multiple receptor conformations for ensemble docking. To evaluate the performance of BP-Dock, we applied our approach on a large and diverse data set using unbound structures as receptors. We also compared the BP-Dock results with bound and unbound docking, where overall receptor flexibility was not taken into account. Our results highlight the importance of modeling backbone flexibility in docking for recapitulating the experimental binding affinities, especially when an unbound structure is used. With BP-Dock, we can generate a wide range of binding site conformations realized in nature even in the absence of a ligand that can help us to improve the accuracy of unbound docking. We expect that our fast and efficient flexible docking approach may further aid in our understanding of protein–ligand interactions as well as virtual screening of novel targets for rational drug design. PMID:24380381

AnchorDock for Blind Flexible Docking of Peptides to Proteins.

PubMed

Slutzki, Michal; Ben-Shimon, Avraham; Niv, Masha Y

2017-01-01

Due to increasing interest in peptides as signaling modulators and drug candidates, several methods for peptide docking to their target proteins are under active development. The "blind" docking problem, where the peptide-binding site on the protein surface is unknown, presents one of the current challenges in the field. AnchorDock protocol was developed by Ben-Shimon and Niv to address this challenge.This protocol narrows the docking search to the most relevant parts of the conformational space. This is achieved by pre-folding the free peptide and by computationally detecting anchoring spots on the surface of the unbound protein. Multiple flexible simulated annealing molecular dynamics (SAMD) simulations are subsequently carried out, starting from pre-folded peptide conformations, constrained to the various precomputed anchoring spots.Here, AnchorDock is demonstrated using two known protein-peptide complexes. A PDZ-peptide complex provides a relatively easy case due to the relatively small size of the protein, and a typical peptide conformation and binding region; a more challenging example is a complex between USP7 N-term and a p53-derived peptide, where the protein is larger, and the peptide conformation and a binding site are generally assumed to be unknown. AnchorDock returned native-like solutions ranked first and third for the PDZ and USP7 complexes, respectively. We describe the procedure step by step and discuss possible modifications where applicable.

DockTrina: docking triangular protein trimers.

PubMed

Popov, Petr; Ritchie, David W; Grudinin, Sergei

2014-01-01

In spite of the abundance of oligomeric proteins within a cell, the structural characterization of protein-protein interactions is still a challenging task. In particular, many of these interactions involve heteromeric complexes, which are relatively difficult to determine experimentally. Hence there is growing interest in using computational techniques to model such complexes. However, assembling large heteromeric complexes computationally is a highly combinatorial problem. Nonetheless the problem can be simplified greatly by considering interactions between protein trimers. After dimers and monomers, triangular trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) are the most frequently observed quaternary structural motifs according to the three-dimensional (3D) complex database. This article presents DockTrina, a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers. The method takes as input pair-wise contact predictions from a rigid body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation test. Finally, it ranks the predictions using a scoring function which combines triples of pair-wise contact terms and a geometric clash penalty term. The overall approach takes less than 2 min per complex on a modern desktop computer. The method is tested and validated using a benchmark set of 220 bound and seven unbound protein trimer structures. DockTrina will be made available at http://nano-d.inrialpes.fr/software/docktrina. Copyright © 2013 Wiley Periodicals, Inc.

Effects of Harbor Modification on Crescent City, California's Tsunami Vulnerability

NASA Astrophysics Data System (ADS)

Dengler, Lori; Uslu, Burak

2011-06-01

More damaging tsunamis have impacted Crescent City, California in historic times than any other location on the West Coast of the USA. Crescent City's harbor has undergone significant modification since the early 20th century, including construction of several breakwaters, dredging, and a 200 × 300 m2 small boat basin. In 2006, a M w 8.3 earthquake in the Kuril Islands generated a moderate Pacific-wide tsunami. Crescent City recorded the highest amplitudes of any tide gauge in the Pacific and was the only location to experience structural damage. Strong currents damaged docks and boats within the small boat basin, causing more than US 20 million in damage and replacement costs. We examine how modifications to Crescent City's harbor may have affected its vulnerability to moderate tsunamis such as the 2006 event. A bathymetric grid of the basin was constructed based on US Army Corps of Engineers soundings in 1964 and 1965 before the construction of the small boat basin. The method of splitting tsunamis was used to estimate tsunami water heights and current velocities at several locations in the harbor using both the 1964-1965 grid and the 2006 bathymetric grid for the 2006 Kuril event and a similar-sized source along the Sanriku coast of Japan. Model velocity outputs are compared for the two different bathymetries at the tide gauge location and at six additional computational sites in the harbor. The largest difference between the two grids is at the small boat basin entrance, where the 2006 bathymetry produces currents over three times the strength of the currents produced by the 1965 bathymetry. Peak currents from a Sanriku event are comparable to those produced by the 2006 event, and within the boat basin may have been higher. The modifications of the harbor, and in particular the addition of the small boat basin, appear to have contributed to the high current velocities and resulting damage in 2006 and help to explain why the 1933 M w 8.4-8.7 Sanriku tsunami

CovalentDock Cloud: a web server for automated covalent docking.

PubMed

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-07-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/.

CovalentDock Cloud: a web server for automated covalent docking

PubMed Central

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-01-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/. PMID:23677616

Pollutant Concentrations and Toxic Effects on the Red Alga Ceramium tenuicorne of Sediments from Natural Harbors and Small Boat Harbors on the West Coast of Sweden.

PubMed

Eklund, Britta; Hansson, Tomas; Bengtsson, Henrik; Eriksson Wiklund, Ann-Kristin

2016-04-01

This investigation set out to analyze the toxicity of surface sediments in a number of natural harbors and small boat harbors on the west coast of Sweden. This was done with the growth inhibition method with Ceramium tenuicorne. Also, concentrations of copper (Cu), lead (Pb), zinc (Zn), irgarol, organotin compounds, and polycyclic aromatic hydrocarbons (PAHs) in the sediments were analyzed. The small boat harbors were heavily polluted by Cu, Zn, butyltins, and PAHs, and to a lesser extent by Pb. The Cu, Pb, Zn, and butyltins probably originated from their past and/or present use in antifouling paints, whereas the PAHs probably had multiple sources, including boat motor exhausts. The measured toxicity of the sediment was generally related to their Cu, Zn, and butyltin content, although other toxic substances than those analyzed here probably contributed to the toxicity in some of the harbors. The natural harbor sediments contained less pollutants and were less toxic than the small boat harbor sediments. Nevertheless, our data indicate that the boating pressure today may be high enough to produce toxic effects even in natural harbors in pristine areas. The strongest relationship between toxicity and the major pollutants was obtained when the sediment toxicity was expressed as gram wet weight per liter compared with gram dry weight per liter and gram total organic carbon per liter. Hence, for pollutants that can be elutriated with natural sea water, sediment toxicity expressed as gram wet weight per liter appears preferable.

Design and Preliminary Testing of the International Docking Adapter's Peripheral Docking Target

NASA Technical Reports Server (NTRS)

Foster, Christopher W.; Blaschak, Johnathan; Eldridge, Erin A.; Brazzel, Jack P.; Spehar, Peter T.

2015-01-01

The International Docking Adapter's Peripheral Docking Target (PDT) was designed to allow a docking spacecraft to judge its alignment relative to the docking system. The PDT was designed to be compatible with relative sensors using visible cameras, thermal imagers, or Light Detection and Ranging (LIDAR) technologies. The conceptual design team tested prototype designs and materials to determine the contrast requirements for the features. This paper will discuss the design of the PDT, the methodology and results of the tests, and the conclusions pertaining to PDT design that were drawn from testing.

Effect of harbor modifications on the tsunami vulnerability of Crescent City, California

NASA Astrophysics Data System (ADS)

Dengler, L.; Uslu, B.

2008-12-01

Crescent City, California has experienced more damaging tsunami events in historic times than any other location on the West Coast of the United States. Thirty-one tsunamis have been observed at Crescent City since a tide gauge was established in 1933, including eleven events with maximum peak to trough wave range exceeding one meter and four that caused damage. The most damaging event occurred in 1964 as a result of the great Alaska earthquake. The ensuing tsunami flooded 29 city blocks and killed 11 in the Crescent City area. As a result of the 1964 tsunami and redevelopment projects, the Crescent City harbor was significantly modified in the early 1970s. A 200 x 300 meter small boat basin was carved into the preexisting shore line, a 123 meter dog leg extension was added to the central breakwater and significant deepening occurred on the eastern side of the harbor. In 2006, a Mw 8.3 earthquake in the Kuril Islands generated a moderate Pacific-wide tsunami. The only location with significant damage was the Crescent City harbor where strong currents damaged docks and boats, causing an estimated 9.2 million (US dollars) in damages. Strong currents estimated by the Harbor Master at 12 knots were observed near the entrance to the small boat basin. Past earthquakes from the northwestern Pacific including the 1933 M 8.3 Sanriku Japan earthquake may have produced similar amplitudes at Crescent City to the 2006 event but caused no damage. We have obtained the pre-modification harbor bathymetry and use the MOST model to compare tsunami water heights and current velocities for the 1933 and 2006 sources using modern and pre- modification bathymetry. We also examine model the 1964 inundation using the actual bathymetry and compare the results to numerical simulations that have only used the modern data.

Apollo Rendezvous Docking Simulator

NASA Image and Video Library

1964-11-02

Originally the Rendezvous was used by the astronauts preparing for Gemini missions. The Rendezvous Docking Simulator was then modified and used to develop docking techniques for the Apollo program. The pilot is shown maneuvering the LEM into position for docking with a full-scale Apollo Command Module. From A.W. Vogeley, Piloted Space-Flight Simulation at Langley Research Center, Paper presented at the American Society of Mechanical Engineers, 1966 Winter Meeting, New York, NY, November 27 - December 1, 1966. The Rendezvous Docking Simulator and also the Lunar Landing Research Facility are both rather large moving-base simulators. It should be noted, however, that neither was built primarily because of its motion characteristics. The main reason they were built was to provide a realistic visual scene. A secondary reason was that they would provide correct angular motion cues (important in control of vehicle short-period motions) even though the linear acceleration cues would be incorrect. Apollo Rendezvous Docking Simulator: Langley s Rendezvous Docking Simulator was developed by NASA scientists to study the complex task of docking the Lunar Excursion Module with the Command Module in Lunar orbit.

Butyltin compounds in sediments from the commercial harbor of Alexandria City, Egypt.

PubMed

Barakat, A O; Kim, M; Qian, Y; Wade, T L

2001-12-01

Tributyltin (TBT), dibutyltin (DBT), and monobutyltin (MBT) compounds were quantitatively determined in surface-sediment samples collected from 23 sites in the commercial harbor of Alexandria City, Egypt. Butyltin concentrations in sediments varied widely depending on the sample location, ranging from less than 0.1 to 186 ng g(-1) of Sn for MBT, less than 0.1 to 379 ng g(-1) of Sn for DBT, and 1 to 2,067 ng g(-1) of Sn for TBT Elevated TBT concentrations, ranging from 727 to 2,067 ng g(-1) of Sn were observed in harbors, marinas, and near ship-repair facilities, indicating that the butyltin-containing, antifouling paints of boats and vessels are the major source of butyltin contamination. The TBT concentration decreased rapidly away from potential source areas of boat docking and repair facilities. The high relative concentrations of TBT in the sediments indicated that degradation processes in the sediments are minor, probably due to the anoxic sedimentary conditions at the sampling sites and/or relatively fresh input of TBT to these sites.

Looking Southwest to Dry and Wet Exterior Scrubbers at Rear ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Looking Southwest to Dry and Wet Exterior Scrubbers at Rear of Oxide Building - Hematite Fuel Fabrication Facility, Oxide Building & Oxide Loading Dock, 3300 State Road P, Festus, Jefferson County, MO

Rendezvous Docking Simulator

NASA Image and Video Library

1964-10-29

Originally the Rendezvous was used by the astronauts preparing for Gemini missions. The Rendezvous Docking Simulator was then modified and used to develop docking techniques for the Apollo program. "The LEM pilot's compartment, with overhead window and the docking ring (idealized since the pilot cannot see it during the maneuvers), is shown docked with the full-scale Apollo Command Module." A.W. Vogeley described the simulator as follows: "The Rendezvous Docking Simulator and also the Lunar Landing Research Facility are both rather large moving-base simulators. It should be noted, however, that neither was built primarily because of its motion characteristics. The main reason they were built was to provide a realistic visual scene. A secondary reason was that they would provide correct angular motion cues (important in control of vehicle short-period motions) even though the linear acceleration cues would be incorrect." -- Published in A.W. Vogeley, "Piloted Space-Flight Simulation at Langley Research Center," Paper presented at the American Society of Mechanical Engineers, 1966 Winter Meeting, New York, NY, November 27 - December 1, 1966;

Electrostatics in protein–protein docking

PubMed Central

Heifetz, Alexander; Katchalski-Katzir, Ephraim; Eisenstein, Miriam

2002-01-01

A novel geometric-electrostatic docking algorithm is presented, which tests and quantifies the electrostatic complementarity of the molecular surfaces together with the shape complementarity. We represent each molecule to be docked as a grid of complex numbers, storing information regarding the shape of the molecule in the real part and information regarding the electrostatic character of the molecule in the imaginary part. The electrostatic descriptors are derived from the electrostatic potential of the molecule. Thus, the electrostatic character of the molecule is represented as patches of positive, neutral, or negative values. The potential for each molecule is calculated only once and stored as potential spheres adequate for exhaustive rotation/translation scans. The geometric-electrostatic docking algorithm is applied to 17 systems, starting form the structures of the unbound molecules. The results—in terms of the complementarity scores of the nearly correct solutions, their ranking in the lists of sorted solutions, and their statistical uniqueness—are compared with those of geometric docking, showing that the inclusion of electrostatic complementarity in docking is very important, in particular in docking of unbound structures. Based on our results, we formulate several "good electrostatic docking rules": The geometric-electrostatic docking procedure is more successful than geometric docking when the potential patches are large and when the potential extends away from the molecular surface and protrudes into the solvent. In contrast, geometric docking is recommended when the electrostatic potential around the molecules to be docked appears homogenous, that is, with a similar sign all around the molecule. PMID:11847280

Spacecraft capture and docking system

NASA Technical Reports Server (NTRS)

Kong, Kinyuen (Inventor); Rafeek, Shaheed (Inventor); Myrick, Thomas (Inventor)

2001-01-01

A system for capturing and docking an active craft to a passive craft has a first docking assembly on the active craft with a first contact member and a spike projecting outwardly, a second docking assembly on the passive craft having a second contact member and a flexible net deployed over a target area with an open mesh for capturing the end of the spike of the active craft, and a motorized net drive for reeling in the net and active craft to mate with the passive craft's docking assembly. The spike has extendable tabs to allow it to become engaged with the net. The net's center is coupled to a net spool for reeling in. An alignment funnel has inclined walls to guide the net and captured spike towards the net spool. The passive craft's docking assembly includes circumferentially spaced preload wedges which are driven to lock the wedges against the contact member of the active craft. The active craft's docking assembly includes a rotary table and drive for rotating it to a predetermined angular alignment position, and mating connectors are then engaged with each other. The system may be used for docking spacecraft in zero or low-gravity environments, as well as for docking underwater vehicles, docking of ancillary craft to a mother craft in subsonic flight, in-flight refueling systems, etc.

VIEW OF FACILITY NO. S 20 NEAR THE POINT WHERE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

VIEW OF FACILITY NO. S 20 NEAR THE POINT WHERE IT JOINS FACILITY NO. S 21. NOTE THE ASPHALT-FILLED NARROW-GAUGE TRACKWAY WITH SOME AREAS OF STEEL TRACK SHOWING. VIEW FACING NORTHEAST - U.S. Naval Base, Pearl Harbor, Floating Dry Dock Quay, Hurt Avenue at northwest side of Magazine Loch, Pearl City, Honolulu County, HI

Compodock, a new device for sterile docking.

PubMed

van Der Meer, P F; Biekart, F T; Pietersz, R N; Rebers, S P; Reesink, H W

2000-06-01

A new device for sterile docking, the Compodock (Fresenius NPBI Transfusion Technology), was developed for connecting PVC tubing for medical use while maintaining sterility. Sterility of the connections was assessed by welding tubing with a heavy exterior contamination with Bacillus subtilis spores and also by welding in an environment contaminated with aerosols of B. subtilis. Tubing was either dry or liquid-filled ("wet") and had various diameters. Bacterial culture medium was flushed through the welded area and subsequently cultured. Tensile strength was measured, and, under semi-routine conditions, Compodock was tested for user friendliness and speed. None of the cultures of welded tubing with exterior contamination showed growth, neither the dry-dry (n = 434) nor the wet-wet connections (n = 622). Cultures were also negative for welds made in the contaminated environment (dry-dry, 67; wet-wet, 55). Tensile strength complied fully with ISO 3826 standards (that is, a force of 20 newtons [N] for 15 sec), with a mean maximal strength ranging from 73 to 100 N, depending on diameter and content of the tubing. The semi-routine handling was regarded as good: welds were easily opened; there were clear instructions and error warnings; and the processing time averaged 52 seconds. The Compodock is able to maintain a functionally closed system, with maintenance of sterility, despite heavy exterior bacterial contamination; tensile strength conformed to ISO standards. Compodock is suitable for routine implementation in the blood bank.

Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system.

PubMed

Kantardjiev, Alexander A

2012-07-01

Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments-the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein-ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html.

Spacecraft Docking System

NASA Technical Reports Server (NTRS)

Ghofranian, Siamak (Inventor); Chuang, Li-Ping Christopher (Inventor); Motaghedi, Pejmun (Inventor)

2016-01-01

A method and apparatus for docking a spacecraft. The apparatus comprises elongate members, movement systems, and force management systems. The elongate members are associated with a docking structure for a spacecraft. The movement systems are configured to move the elongate members axially such that the docking structure for the spacecraft moves. Each of the elongate members is configured to move independently. The force management systems connect the movement systems to the elongate members and are configured to limit a force applied by the each of the elongate members to a desired threshold during movement of the elongate members.

Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem.

PubMed

Ban, Tomohiro; Ohue, Masahito; Akiyama, Yutaka

2018-04-01

The identification of comprehensive drug-target interactions is important in drug discovery. Although numerous computational methods have been developed over the years, a gold standard technique has not been established. Computational ligand docking and structure-based drug design allow researchers to predict the binding affinity between a compound and a target protein, and thus, they are often used to virtually screen compound libraries. In addition, docking techniques have also been applied to the virtual screening of target proteins (inverse docking) to predict target proteins of a drug candidate. Nevertheless, a more accurate docking method is currently required. In this study, we proposed a method in which a predicted ligand-binding site is covered by multiple grids, termed multiple grid arrangement. Notably, multiple grid arrangement facilitates the conformational search for a grid-based ligand docking software and can be applied to the state-of-the-art commercial docking software Glide (Schrödinger, LLC). We validated the proposed method by re-docking with the Astex diverse benchmark dataset and blind binding site situations, which improved the correct prediction rate of the top scoring docking pose from 27.1% to 34.1%; however, only a slight improvement in target prediction accuracy was observed with inverse docking scenarios. These findings highlight the limitations and challenges of current scoring functions and the need for more accurate docking methods. The proposed multiple grid arrangement method was implemented in Glide by modifying a cross-docking script for Glide, xglide.py. The script of our method is freely available online at http://www.bi.cs.titech.ac.jp/mga_glide/. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Orbiter Docking System Installation

NASA Technical Reports Server (NTRS)

1995-01-01

Workers in Orbiter Processing Facility Bay 3 are installing the Orbiter Docking System (ODS) in the payload bay of the orbiter Atlantis (OV-104). The ODS includes an airlock, a supporting truss structure, a docking base, and a Russian-built docking mechanism (uppermost). The ODS is nearly 15 feet (4.6 meters) wide, 6.5 feet (2 meters) long, 13.5 feet (4.1 meters high), and weighs more than 3,500 pounds (1,588 kilograms). It is being installed near the forward end of the orbiter's payload bay and will be connected by a short tunnel to the existing airlock inside the orbiter's pressurized crew cabin.The installation will take about two hours to complete. Later this week, the Spacelab module also will be installed in OV-104's payload bay; it will connect to the ODS via a tunnel. During the first docking between the Space Shuttle Atlantis and the Russian Space Station Mir, the Russian-built docking mechanism on the ODS will be mated to a similar interface on the Krystall module docking port on Mir, allowing crew members to pass back and forth between the two spacecraft. That Shuttle mission, STS-71, is scheduled for liftoff in early June.

Optical Docking Aid Containing Fresnel Lenses

NASA Technical Reports Server (NTRS)

Pierce, Cole J.

1995-01-01

Proposed device provides self-contained visual cues to aid in docking. Similar to devices used to guide pilots in landing on aircraft carriers. Positions and directions of beams of light give observer visual cues of position relative to docking target point. Optical assemblies generate directed, diverging beams of light that, together, mark approach path to docking point. Conceived for use in docking spacecraft at Space Station Freedom, device adapted to numerous industrial docking and alignment applications.

Cameron predicts dry tree production system as the future subsea trend

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1978-06-05

Dry chambers are coming into increasing use in the search for offshore oil. With Subsea Station Cameron, an oil well can be drilled on the ocean floor and then topped with a dry production chamber for shirtsleeve work at the wellhead. Components of the station are described: production Christmas tree, chamber, adapter spool, docking plate, entry hatch, flowline connection, and variable controls. (DLC)

Low Impact Docking System (LIDS)

NASA Technical Reports Server (NTRS)

LaBauve, Tobie E.

2009-01-01

Since 1996, NASA has been developing a docking system that will simplify operations and reduce risks associated with mating spacecraft. This effort has focused on developing and testing an original, reconfigurable, active, closed-loop, force-feedback controlled docking system using modern technologies. The primary objective of this effort has been to design a docking interface that is tunable to the unique performance requirements for all types of mating operations (i.e. docking and berthing, autonomous and piloted rendezvous, and in-space assembly of vehicles, modules and structures). The docking system must also support the transfer of crew, cargo, power, fluid, and data. As a result of the past 10 years of docking system advancement, the Low Impact Docking System or LIDS was developed. The current LIDS design incorporates the lessons learned and development experiences from both previous and existing docking systems. LIDS feasibility was established through multiple iterations of prototype hardware development and testing. Benefits of LIDS include safe, low impact mating operations, more effective and flexible mission implementation with an anytime/anywhere mating capability, system level redundancy, and a more affordable and sustainable mission architecture with reduced mission and life cycle costs. In 1996 the LIDS project, then known as the Advanced Docking Berthing System (ADBS) project, launched a four year developmental period. At the end of the four years, the team had built a prototype of the soft-capture hardware and verified the control system that will be used to control the soft-capture system. In 2001, the LIDS team was tasked to work with the X- 38 Crew Return Vehicle (CRV) project and build its first Engineering Development Unit (EDU).

InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information

PubMed Central

Yu, Jinchao; Vavrusa, Marek; Andreani, Jessica; Rey, Julien; Tufféry, Pierre; Guerois, Raphaël

2016-01-01

The structural modeling of protein–protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/. PMID:27131368

A Hadoop-based Molecular Docking System

NASA Astrophysics Data System (ADS)

Dong, Yueli; Guo, Quan; Sun, Bin

2017-10-01

Molecular docking always faces the challenge of managing tens of TB datasets. It is necessary to improve the efficiency of the storage and docking. We proposed the molecular docking platform based on Hadoop for virtual screening, it provides the preprocessing of ligand datasets and the analysis function of the docking results. A molecular cloud database that supports mass data management is constructed. Through this platform, the docking time is reduced, the data storage is efficient, and the management of the ligand datasets is convenient.

pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.

PubMed

Jiménez-García, Brian; Pons, Carles; Fernández-Recio, Juan

2013-07-01

pyDockWEB is a web server for the rigid-body docking prediction of protein-protein complex structures using a new version of the pyDock scoring algorithm. We use here a new custom parallel FTDock implementation, with adjusted grid size for optimal FFT calculations, and a new version of pyDock, which dramatically speeds up calculations while keeping the same predictive accuracy. Given the 3D coordinates of two interacting proteins, pyDockWEB returns the best docking orientations as scored mainly by electrostatics and desolvation energy. The server does not require registration by the user and is freely accessible for academics at http://life.bsc.es/servlet/pydock. Supplementary data are available at Bioinformatics online.

Gemini rendezvous docking simulator

NASA Image and Video Library

1963-11-04

Multiple exposure of Gemini rendezvous docking simulator. Francis B. Smith wrote in his paper "Simulators for Manned Space Research," "The rendezvous and docking operation of the Gemini spacecraft with the Agena and of the Apollo Command Module with the Lunar Excursion Module have been the subject of simulator studies for several years. [This figure] illustrates the Gemini-Agena rendezvous docking simulator at Langley. The Gemini spacecraft was supported in a gimbal system by an overhead crane and gantry arrangement which provided 6 degrees of freedom - roll, pitch, yaw, and translation in any direction - all controllable by the astronaut in the spacecraft. Here again the controls fed into a computer which in turn provided an input to the servos driving the spacecraft so that it responded to control motions in a manner which accurately simulated the Gemini spacecraft." A.W. Vogeley further described the simulator in his paper "Discussion of Existing and Planned Simulators For Space Research," "Docking operations are considered to start when the pilot first can discern vehicle target size and aspect and terminate, of course, when soft contact is made. ... This facility enables simulation of the docking operation from a distance of 200 feet to actual contact with the target. A full-scale mock-up of the target vehicle is suspended near one end of the track. ... On [the Agena target] we have mounted the actual Agena docking mechanism and also various types of visual aids. We have been able to devise visual aids which have made it possible to accomplish nighttime docking with as much success as daytime docking." -- Published in Barton C. Hacker and James M. Grimwood, On the Shoulders of Titans: A History of Project Gemini, NASA SP-4203; Francis B. Smith, "Simulators for Manned Space Research," Paper presented at the 1966 IEEE International convention, March 21-25, 1966; A.W. Vogeley, "Discussion of Existing and Planned Simulators For Space Research," Paper presented at

Enabling Exploration Through Docking Standards

NASA Technical Reports Server (NTRS)

Hatfield, Caris A.

2012-01-01

Human exploration missions beyond low earth orbit will likely require international cooperation in order to leverage limited resources. International standards can help enable cooperative missions by providing well understood, predefined interfaces allowing compatibility between unique spacecraft and systems. The International Space Station (ISS) partnership has developed a publicly available International Docking System Standard (IDSS) that provides a solution to one of these key interfaces by defining a common docking interface. The docking interface provides a way for even dissimilar spacecraft to dock for exchange of crew and cargo, as well as enabling the assembly of large space systems. This paper provides an overview of the key attributes of the IDSS, an overview of the NASA Docking System (NDS), and the plans for updating the ISS with IDSS compatible interfaces. The NDS provides a state of the art, low impact docking system that will initially be made available to commercial crew and cargo providers. The ISS will be used to demonstrate the operational utility of the IDSS interface as a foundational technology for cooperative exploration.

Russian Docking Module is lowered

NASA Technical Reports Server (NTRS)

1995-01-01

The Russian-built Docking Module (DM) is lowered for installation into the payload bay of the Space Shuttle Orbiter Atlantis while the spaceplane is in Orbiter Processing Facility bay 2. The module will fly as a primary payload on the second Space Shuttle/Mir space station docking mission, STS-74, which is now scheduled for liftoff in the fall of 1995. During the mission, the module will first be attached with the orbiter's robot arm to the Orbiter Docking System (ODS) in the payload bay of the orbiter Atlantis and then be docked with the Mir. When Atlantis undocks from the Mir, it will leave the new docking module permanently attached to the space station for use during future Shuttle Mir docking missions. The new module will simplify future Shuttle linkups with Mir by improving orbiter clearances when it serves as a bridge between the two space vehicles. The white structures attached to the module's sides are solar panels that will be attached to the Mir after the conclusion of the STS-74 mission.

Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server.

PubMed

Karaca, Ezgi; Melquiond, Adrien S J; de Vries, Sjoerd J; Kastritis, Panagiotis L; Bonvin, Alexandre M J J

2010-08-01

Over the last years, large scale proteomics studies have generated a wealth of information of biomolecular complexes. Adding the structural dimension to the resulting interactomes represents a major challenge that classical structural experimental methods alone will have difficulties to confront. To meet this challenge, complementary modeling techniques such as docking are thus needed. Among the current docking methods, HADDOCK (High Ambiguity-Driven DOCKing) distinguishes itself from others by the use of experimental and/or bioinformatics data to drive the modeling process and has shown a strong performance in the critical assessment of prediction of interactions (CAPRI), a blind experiment for the prediction of interactions. Although most docking programs are limited to binary complexes, HADDOCK can deal with multiple molecules (up to six), a capability that will be required to build large macromolecular assemblies. We present here a novel web interface of HADDOCK that allows the user to dock up to six biomolecules simultaneously. This interface allows the inclusion of a large variety of both experimental and/or bioinformatics data and supports several types of cyclic and dihedral symmetries in the docking of multibody assemblies. The server was tested on a benchmark of six cases, containing five symmetric homo-oligomeric protein complexes and one symmetric protein-DNA complex. Our results reveal that, in the presence of either bioinformatics and/or experimental data, HADDOCK shows an excellent performance: in all cases, HADDOCK was able to generate good to high quality solutions and ranked them at the top, demonstrating its ability to model symmetric multicomponent assemblies. Docking methods can thus play an important role in adding the structural dimension to interactomes. However, although the current docking methodologies were successful for a vast range of cases, considering the variety and complexity of macromolecular assemblies, inclusion of some kind of

Expedition 23 Docking

NASA Image and Video Library

2010-04-03

View from the balcony of the Russian Mission Control Center in Korolev, Russia as the Soyuz TMA-18 docks to the International Space Station on Sunday, April 4, 2010. The Soyuz TMA-18 docked to the International Space Station carrying Expedition 23 Soyuz Commander Alexander Skvortsov, Flight Engineer Mikhail Kornienko and NASA Flight Engineer Tracy Caldwell Dyson. Photo Credit: (NASA/Carla Cioffi)

Ginger (Zingiber officinale) phytochemicals-gingerenone-A and shogaol inhibit SaHPPK: molecular docking, molecular dynamics simulations and in vitro approaches.

PubMed

Rampogu, Shailima; Baek, Ayoung; Gajula, Rajesh Goud; Zeb, Amir; Bavi, Rohit S; Kumar, Raj; Kim, Yongseong; Kwon, Yong Jung; Lee, Keun Woo

2018-04-02

Antibiotic resistance is a defense mechanism, harbored by pathogens to survive under unfavorable conditions. Among several antibiotic resistant microbial consortium, Staphylococcus aureus is one of the most havoc microorganisms. Staphylococcus aureus encodes a unique enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (SaHPPK), against which, none of existing antibiotics have been reported. Computational approaches have been instrumental in designing and discovering new drugs for several diseases. The present study highlights the impact of ginger phytochemicals on Staphylococcus aureus SaHPPK. Herein, we have retrieved eight ginger phytochemicals from published literature and investigated their inhibitory interactions with SaHPPK. To authenticate our work, the investigation proceeds considering the known antibiotics alongside the phytochemicals. Molecular docking was performed employing GOLD and CDOCKER. The compounds with the highest dock score from both the docking programmes were tested for their inhibitory capability in vitro. The binding conformations that were seated within the binding pocket showing strong interactions with the active sites residues rendered by highest dock score were forwarded towards the molecular dynamic (MD) simulation analysis. Based on molecular dock scores, molecular interaction with catalytic active residues and MD simulations studies, two ginger phytochemicals, gingerenone-A and shogaol have been proposed as candidate inhibitors against Staphylococcus aureus. They have demonstrated higher dock scores than the known antibiotics and have represented interactions with the key residues within the active site. Furthermore, these compounds have rendered considerable inhibitory activity when tested in vitro. Additionally, their superiority was corroborated by stable MD results conducted for 100 ns employing GROMACS package. Finally, we suggest that gingerenone-A and shogaol may either be potential SaHPPK inhibitors or can be used

Protein docking prediction using predicted protein-protein interface.

PubMed

Li, Bin; Kihara, Daisuke

2012-01-10

Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm), is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

Estuarine studies in upper Grays Harbor, Washington

USGS Publications Warehouse

Beverage, Joseph P.; Swecker, Milton N.

1969-01-01

. The carbon content of bottom materials was related to channel fine material: C= 0.315+0.0238 F where C is in percent by dry weight, and F is percent by weight finer than 0.062 millimeter. Carbon content was low upstream and downstream of the upper harbor area, and high in the Cow Point-Rennie Island reach. The high-carbon-content reach coincides with the general area of a dissolved-oxygen sag. The logarithm of the fresh-water discharge gave a high degree of correlation with daily maximum specific conductance at Cosmopolis. The regression equation is: Kc max---- 76.4-- 17.7 logl0 Qf where Kc max is in millimhos at 25 ? Celsius (centigrade), and Qf is the estimated daily fresh-water discharge, in cubic feet per second. Dissolved oxygen is the most critical water-quality parameter in Grays Harbor. At Cosmopolis, the daily minimum dissolved oxygen content, DOc min, correlated well with discharge and tidal range, delta H. The regression equation relating the variables is: DOc min---- 6.03 + 0.00096 Qf - 0.291 delta H in which DOc min is in milligrams per liter and delta H is in feet. The upper harbor was found to contain 250 million cubic feet less water than average during the critical low-flow period, on the basis of the frequency distribution of predicted tides. About 78,000 pounds of dissolved oxygen is thus unavailable for oxidation of waste during summer.

Expedition 27 Docking

NASA Image and Video Library

2011-04-06

Top officials from the Russian Federal Space Agency and NASA hold a Soyuz post-docking press conference at the Russian Mission Control Center in Korolev, Russia on Thursday, April 7, 2011. The Soyuz TMA-21 docked to the International Space Station carrying Expedition 27 Soyuz Commander Alexander Samokutyaev, NASA Flight Engineer Ron Garan and Russian Flight Engineer Andrey Borisenko. Photo Credit: (NASA/Carla Cioffi)

Expedition 23 Docking

NASA Image and Video Library

2010-04-03

Kirk Shireman, NASA's deputy ISS program manager, answers reporter’s questions during a Soyuz post-docking press conference at the Russian Mission Control Center in Korolev, Russia on Sunday, April 4, 2010. The Soyuz TMA-18 docked to the International Space Station carrying Expedition 23 Soyuz Commander Alexander Skvortsov, Flight Engineer Mikhail Kornienko and NASA Flight Engineer Tracy Caldwell Dyson. Photo Credit: (NASA/Carla Cioffi)

Expedition 23 Docking

NASA Image and Video Library

2010-04-03

Kirk Shireman, right, NASA's deputy ISS program manager, answers reporter’s questions during a Soyuz post-docking press conference at the Russian Mission Control Center in Korolev, Russia on Sunday, April 4, 2010. The Soyuz TMA-18 docked to the International Space Station carrying Expedition 23 Soyuz Commander Alexander Skvortsov, Flight Engineer Mikhail Kornienko and NASA Flight Engineer Tracy Caldwell Dyson. Photo Credit: (NASA/Carla Cioffi)

InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs.

PubMed

Quignot, Chloé; Rey, Julien; Yu, Jinchao; Tufféry, Pierre; Guerois, Raphaël; Andreani, Jessica

2018-05-08

Computational protein docking is a powerful strategy to predict structures of protein-protein interactions and provides crucial insights for the functional characterization of macromolecular cross-talks. We previously developed InterEvDock, a server for ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking. InterEvDock2 is a major evolution of InterEvDock which allows users to submit input sequences - not only structures - and multimeric inputs and to specify constraints for the pairwise docking process based on previous knowledge about the interaction. For this purpose, we added modules in InterEvDock2 for automatic template search and comparative modeling of the input proteins. The InterEvDock2 pipeline was benchmarked on 812 complexes for which unbound homology models of the two partners and co-evolutionary information are available in the PPI4DOCK database. InterEvDock2 identified a correct model among the top 10 consensus in 29% of these cases (compared to 15-24% for individual scoring functions) and at least one correct interface residue among 10 predicted in 91% of these cases. InterEvDock2 is thus a unique protein docking server, designed to be useful for the experimental biology community. The InterEvDock2 web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/.

Multilevel Parallelization of AutoDock 4.2.

PubMed

Norgan, Andrew P; Coffman, Paul K; Kocher, Jean-Pierre A; Katzmann, David J; Sosa, Carlos P

2011-04-28

Virtual (computational) screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing molecular docking, the prediction of ligand-receptor interactions. AutoDock is a serial application, though several previous efforts have parallelized various aspects of the program. In this paper, we report on a multi-level parallelization of AutoDock 4.2 (mpAD4). Using MPI and OpenMP, AutoDock 4.2 was parallelized for use on MPI-enabled systems and to multithread the execution of individual docking jobs. In addition, code was implemented to reduce input/output (I/O) traffic by reusing grid maps at each node from docking to docking. Performance of mpAD4 was examined on two multiprocessor computers. Using MPI with OpenMP multithreading, mpAD4 scales with near linearity on the multiprocessor systems tested. In situations where I/O is limiting, reuse of grid maps reduces both system I/O and overall screening time. Multithreading of AutoDock's Lamarkian Genetic Algorithm with OpenMP increases the speed of execution of individual docking jobs, and when combined with MPI parallelization can significantly reduce the execution time of virtual screens. This work is significant in that mpAD4 speeds the execution of certain molecular docking workloads and allows the user to optimize the degree of system-level (MPI) and node-level (OpenMP) parallelization to best fit both workloads and computational resources.

Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.

PubMed

Wu, Guosheng; Robertson, Daniel H; Brooks, Charles L; Vieth, Michal

2003-10-01

The influence of various factors on the accuracy of protein-ligand docking is examined. The factors investigated include the role of a grid representation of protein-ligand interactions, the initial ligand conformation and orientation, the sampling rate of the energy hyper-surface, and the final minimization. A representative docking method is used to study these factors, namely, CDOCKER, a molecular dynamics (MD) simulated-annealing-based algorithm. A major emphasis in these studies is to compare the relative performance and accuracy of various grid-based approximations to explicit all-atom force field calculations. In these docking studies, the protein is kept rigid while the ligands are treated as fully flexible and a final minimization step is used to refine the docked poses. A docking success rate of 74% is observed when an explicit all-atom representation of the protein (full force field) is used, while a lower accuracy of 66-76% is observed for grid-based methods. All docking experiments considered a 41-member protein-ligand validation set. A significant improvement in accuracy (76 vs. 66%) for the grid-based docking is achieved if the explicit all-atom force field is used in a final minimization step to refine the docking poses. Statistical analysis shows that even lower-accuracy grid-based energy representations can be effectively used when followed with full force field minimization. The results of these grid-based protocols are statistically indistinguishable from the detailed atomic dockings and provide up to a sixfold reduction in computation time. For the test case examined here, improving the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures. Copyright 2003 Wiley Periodicals, Inc.

DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015

NASA Astrophysics Data System (ADS)

Salmaso, Veronica; Sturlese, Mattia; Cuzzolin, Alberto; Moro, Stefano

2016-09-01

Structure-based drug design (SBDD) has matured within the last two decades as a valuable tool for the optimization of low molecular weight lead compounds to highly potent drugs. The key step in SBDD requires knowledge of the three-dimensional structure of the target-ligand complex, which is usually determined by X-ray crystallography. In the absence of structural information for the complex, SBDD relies on the generation of plausible molecular docking models. However, molecular docking protocols suffer from inaccuracies in the description of the interaction energies between the ligand and the target molecule, and often fail in the prediction of the correct binding mode. In this context, the appropriate selection of the most accurate docking protocol is absolutely relevant for the final molecular docking result, even if addressing this point is absolutely not a trivial task. D3R Grand Challenge 2015 has represented a precious opportunity to test the performance of DockBench, an integrate informatics platform to automatically compare RMDS-based molecular docking performances of different docking/scoring methods. The overall performance resulted in the blind prediction are encouraging in particular for the pose prediction task, in which several complex were predicted with a sufficient accuracy for medicinal chemistry purposes.

DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015.

PubMed

Salmaso, Veronica; Sturlese, Mattia; Cuzzolin, Alberto; Moro, Stefano

2016-09-01

Structure-based drug design (SBDD) has matured within the last two decades as a valuable tool for the optimization of low molecular weight lead compounds to highly potent drugs. The key step in SBDD requires knowledge of the three-dimensional structure of the target-ligand complex, which is usually determined by X-ray crystallography. In the absence of structural information for the complex, SBDD relies on the generation of plausible molecular docking models. However, molecular docking protocols suffer from inaccuracies in the description of the interaction energies between the ligand and the target molecule, and often fail in the prediction of the correct binding mode. In this context, the appropriate selection of the most accurate docking protocol is absolutely relevant for the final molecular docking result, even if addressing this point is absolutely not a trivial task. D3R Grand Challenge 2015 has represented a precious opportunity to test the performance of DockBench, an integrate informatics platform to automatically compare RMDS-based molecular docking performances of different docking/scoring methods. The overall performance resulted in the blind prediction are encouraging in particular for the pose prediction task, in which several complex were predicted with a sufficient accuracy for medicinal chemistry purposes.

Expedition 28 Docking

NASA Image and Video Library

2011-06-10

Top officials from the Russian Federal Space Agency and NASA hold a Soyuz post-docking press conference at the Russian Mission Control Center in Korolev, Russia on Friday, June 10, 2011. The Soyuz TMA-02M docked to the International Space Station carrying Expedition 28 Soyuz Commander Sergei Volkov, NASA Flight Engineer Mike Fossum and JAXA (Japanase Aerospace Exploration Agency) Flight Engineer Satoshi Furukawa. Photo Credit: (NASA/Carla Cioffi)

Expedition 23 Docking

NASA Image and Video Library

2010-04-03

Alexei Krasnov, Director of Manned Space Programs Department, Roscosmos, listens to reporter’s questions during a Soyuz post-docking press conference at the Russian mission Control Center in Korolev, Russia on Sunday, April 4, 2010. The Soyuz TMA-18 docked to the International Space Station carrying Expedition 23 Soyuz Commander Alexander Skvortsov, Flight Engineer Mikhail Kornienko and NASA Flight Engineer Tracy Caldwell Dyson. Photo Credit: (NASA/Carla Cioffi)

AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking.

PubMed

Uehara, Shota; Tanaka, Shigenori

2016-11-23

Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water molecules are substantially different from those of waters in the bulk region. The binding of a ligand to a protein causes a displacement of these waters from an active site to bulk, and this displacement process substantially contributes to the free energy change of protein-ligand binding. The free energy of active-site water molecules can be calculated by grid inhomogeneous solvation theory (GIST), using molecular dynamics (MD) and the trajectory of a target protein and water molecules. Here, we show a case study of the combination of GIST and a docking program and discuss the effectiveness of the displacing gain of unfavorable water in protein-ligand docking. We combined the GIST-based desolvation function with the scoring function of AutoDock4, which is called AutoDock-GIST. The proposed scoring function was assessed employing 51 ligands of coagulation factor Xa (FXa), and results showed that both scoring accuracy and docking success rate were improved. We also evaluated virtual screening performance of AutoDock-GIST using FXa ligands in the directory of useful decoys-enhanced (DUD-E), thus finding that the displacing gain of unfavorable water is effective for a successful docking campaign.

Satellite Docking Simulator with Generic Contact Dynamics Capabilities

NASA Astrophysics Data System (ADS)

Ma, O.; Crabtree, D.; Carr, R.; Gonthier, Y.; Martin, E.; Piedboeuf, J.-C.

2002-01-01

Satellite docking (and capture) systems are critical for the servicing or salvage of satellites. Satellite servicing has comparatively recently become a realistic and promising space operation/mission. Satellite servicing includes several of the following operations: rendezvous; docking (capturing); inspection; towing (transporting); refueling; refurbishing (replacement of faulty or "used-up" modules/boxes); and un-docking (releasing). Because spacecraft servicing has been, until recently non-feasible or non-economical, spacecraft servicing technology has been neglected. Accordingly, spacecraft designs have featured self- contained systems without consideration for operational servicing. Consistent with this view, most spacecrafts were designed and built without docking interfaces. If, through some mishap, a spacecraft was rendered non-operational, it was simply considered expendable. Several feasibility studies are in progress on salvaging stranded satellites (which, in fact had led to this project). The task of the designer of the docking system for a salvaging task is difficult. He/she has to work with whatever it is on orbit, and this excludes any special docking interfaces, which might have made his/her task easier. As satellite servicing becomes an accepted design requirement, many future satellites will be equipped with appropriate docking interfaces. The designer of docking systems will be faced with slightly different challenges: reliable, cost-effective, docking (and re-supply) systems. Thus, the role of designers of docking systems will increase from one of a kind, ad-hoc interfaces intended for salvaging operations, to docking systems for satellites and "caretaker" spacecraft which are meant for servicing and are produced in larger numbers. As in any space system (for which full and representative ground hardware test-beds are very expensive and often impossible to develop), simulations are mandatory for the development of systems and operations for

Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking.

PubMed

Yan, Yumeng; Wen, Zeyu; Wang, Xinxiang; Huang, Sheng-You

2017-03-01

Protein-protein docking is an important computational tool for predicting protein-protein interactions. With the rapid development of proteomics projects, more and more experimental binding information ranging from mutagenesis data to three-dimensional structures of protein complexes are becoming available. Therefore, how to appropriately incorporate the biological information into traditional ab initio docking has been an important issue and challenge in the field of protein-protein docking. To address these challenges, we have developed a Hybrid DOCKing protocol of template-based and template-free approaches, referred to as HDOCK. The basic procedure of HDOCK is to model the structures of individual components based on the template complex by a template-based method if a template is available; otherwise, the component structures will be modeled based on monomer proteins by regular homology modeling. Then, the complex structure of the component models is predicted by traditional protein-protein docking. With the HDOCK protocol, we have participated in the CPARI experiment for rounds 28-35. Out of the 25 CASP-CAPRI targets for oligomer modeling, our HDOCK protocol predicted correct models for 16 targets, ranking one of the top algorithms in this challenge. Our docking method also made correct predictions on other CAPRI challenges such as protein-peptide binding for 6 out of 8 targets and water predictions for 2 out of 2 targets. The advantage of our hybrid docking approach over pure template-based docking was further confirmed by a comparative evaluation on 20 CASP-CAPRI targets. Proteins 2017; 85:497-512. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

33 CFR 100.109 - Winter Harbor Lobster Boat Race, Winter Harbor, ME.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Winter Harbor Lobster Boat Race, Winter Harbor, ME. 100.109 Section 100.109 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Lobster Boat Race, Winter Harbor, ME. (a) Regulated area. The regulated area includes all waters of Winter...

Expedition 28 Docking

NASA Image and Video Library

2011-06-10

Vladimir Popovkin, Head of the Russian Federal Space Agency (ROSCOSMOS) answers a reporter’s question during a Soyuz post-docking press conference at the Russian Mission Control Center in Korolev, Russia on Friday, June 10, 2011. The Soyuz TMA-02M docked to the International Space Station carrying Expedition 28 Soyuz Commander Sergei Volkov, NASA Flight Engineer Mike Fossum and JAXA (Japanase Aerospace Exploration Agency) Flight Engineer Satoshi Furukawa. Photo Credit: (NASA/Carla Cioffi)

Expedition 28 Docking

NASA Image and Video Library

2011-06-10

William Gerstenmaier, Associate Administrator for Space Operations, is interviewed by Russian Federal Space Agency (ROSCOSMOS) TV following a Soyuz post-docking press conference at the Russian Mission Control Center in Korolev, Russia on Friday, June 10, 2011. The Soyuz TMA-02M docked to the International Space Station carrying Expedition 28 Soyuz Commander Sergei Volkov, NASA Flight Engineer Mike Fossum and JAXA (Japanase Aerospace Exploration Agency) Flight Engineer Satoshi Furukawa. Photo Credit: (NASA/Carla Cioffi)

Expedition 27 Docking

NASA Image and Video Library

2011-04-06

Russian Federal Space Agency Director of Human Space Flight, Alexey Krasnov, third from right, answers reporter’s questions during a Soyuz post-docking press conference at the Russian Mission Control Center in Korolev, Russia on Thursday, April 7, 2011. The Soyuz TMA-21 docked to the International Space Station carrying Expedition 27 Soyuz Commander Alexander Samokutyaev, NASA Flight Engineer Ron Garan and Russian Flight Engineer Andrey Borisenko. Photo Credit: (NASA/Carla Cioffi)

Expedition 26 Docking

NASA Image and Video Library

2010-12-18

Vitaly Davyidov, second from right, Deputy Head of the Russian Federal Space Agency, answers reporter’s questions during a Soyuz post-docking press conference at the Russian Mission Control Center in Korolev, Russia on Saturday, Dec. 18, 2010. The Soyuz TMA-20 docked to the International Space Station carrying Expedition 26 Soyuz Commander Dmitry Kondratyev, Flight Engineer Catherine Coleman and European Space Agency Flight Engineer Paolo Nespoli. Photo Credit: (NASA/Carla Cioffi)

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.

PubMed

Kurcinski, Mateusz; Jamroz, Michal; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

2015-07-01

Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein-peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

PubMed Central

Kurcinski, Mateusz; Jamroz, Michal; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

2015-01-01

Protein–peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein–peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein–peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. PMID:25943545

Smart tunnel: Docking mechanism

NASA Technical Reports Server (NTRS)

Schliesing, John A. (Inventor); Edenborough, Kevin L. (Inventor)

1989-01-01

A docking mechanism is presented for the docking of a space vehicle to a space station comprising a flexible tunnel frame structure which is deployable from the space station. The tunnel structure comprises a plurality of series connected frame sections, one end section of which is attached to the space station and the other end attached to a docking module of a configuration adapted for docking in the payload bay of the space vehicle. The docking module is provided with trunnions, adapted for latching engagement with latches installed in the vehicle payload bay and with hatch means connectable to a hatch of the crew cabin of the space vehicle. Each frame section comprises a pair of spaced ring members, interconnected by actuator-attenuator devices which are individually controllable by an automatic control means to impart relative movement of one ring member to the other in six degrees of freedom of motion. The control means includes computer logic responsive to sensor signals of range and attitude information, capture latch condition, structural loads, and actuator stroke for generating commands to the onboard flight control system and the individual actuator-attenuators to deploy the tunnel to effect a coupling with the space vehicle and space station after coupling. A tubular fluid-impervious liner, preferably fabric, is disposed through the frame sections of a size sufficient to accommodate the passage of personnel and cargo.

PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets.

PubMed

Yu, Jinchao; Guerois, Raphaël

2016-12-15

Protein-protein docking methods are of great importance for understanding interactomes at the structural level. It has become increasingly appealing to use not only experimental structures but also homology models of unbound subunits as input for docking simulations. So far we are missing a large scale assessment of the success of rigid-body free docking methods on homology models. We explored how we could benefit from comparative modelling of unbound subunits to expand docking benchmark datasets. Starting from a collection of 3157 non-redundant, high X-ray resolution heterodimers, we developed the PPI4DOCK benchmark containing 1417 docking targets based on unbound homology models. Rigid-body docking by Zdock showed that for 1208 cases (85.2%), at least one correct decoy was generated, emphasizing the efficiency of rigid-body docking in generating correct assemblies. Overall, the PPI4DOCK benchmark contains a large set of realistic cases and provides new ground for assessing docking and scoring methodologies. Benchmark sets can be downloaded from http://biodev.cea.fr/interevol/ppi4dock/ CONTACT: guerois@cea.frSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Detail of pier structure and wood fenders of Facility No. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Detail of pier structure and wood fenders of Facility No. B-1, showing floats in foreground and bollards on pier, view facing east - U.S. Naval Base, Pearl Harbor, South Quay Wall & Repair Wharf, L-shaped portion of quay walls starting at east side of mouth of Dry Dock No. 1, continuing along ocean side of Sixth Street, adjacent to Pier B-2, Pearl City, Honolulu County, HI

Were Viking Dry-dock methods in the Americas used earlier to Build Pyramids, with Outflow Eroding the Sphinx, and were Stonehenge, the Obelisks, and Moas Similarly Erected?

NASA Astrophysics Data System (ADS)

McLeod, Edward; McLeod, Roger

2006-03-01

Chisel-quarried recycled granite in MA is datable by runes to 1069 CE; it could corroborate dating by a LIDAR. Associated sites, possibly used by Vikings to dry-dock their ships, could have exploited lock-like controls, possibly a continued technology. Site-leveling at the Giza Pyramids proves water was used. `Locks' and body-immersion worked for building, moving, erecting, or watering, at sites like Stonehenge, The Hanging Gardens at Babylon, the Moas of Easter Island, or The Pyramids, where the eroding water discharge was deliberately flushed over the Sphinx complex. It enhance the electromagnetically excited blue light signals we can detect, especially at sites frequented by Molocket of ME. Information, as at America's Stonehenge, in NH, and constructions at Acton MA, at Giza or at Rumford ME proves that the Pyramids and Sphinx were engineered and built about 4500 BP.

Multi-Conformer Ensemble Docking to Difficult Protein Targets

DOE PAGES

Ellingson, Sally R.; Miao, Yinglong; Baudry, Jerome; ...

2014-09-08

We investigate large-scale ensemble docking using five proteins from the Directory of Useful Decoys (DUD, dud.docking.org) for which docking to crystal structures has proven difficult. Molecular dynamics trajectories are produced for each protein and an ensemble of representative conformational structures extracted from the trajectories. Docking calculations are performed on these selected simulation structures and ensemble-based enrichment factors compared with those obtained using docking in crystal structures of the same protein targets or random selection of compounds. We also found simulation-derived snapshots with improved enrichment factors that increased the chemical diversity of docking hits for four of the five selected proteins.more » A combination of all the docking results obtained from molecular dynamics simulation followed by selection of top-ranking compounds appears to be an effective strategy for increasing the number and diversity of hits when using docking to screen large libraries of chemicals against difficult protein targets.« less

Automated Docking Screens: A Feasibility Study

PubMed Central

2009-01-01

Molecular docking is the most practical approach to leverage protein structure for ligand discovery, but the technique retains important liabilities that make it challenging to deploy on a large scale. We have therefore created an expert system, DOCK Blaster, to investigate the feasibility of full automation. The method requires a PDB code, sometimes with a ligand structure, and from that alone can launch a full screen of large libraries. A critical feature is self-assessment, which estimates the anticipated reliability of the automated screening results using pose fidelity and enrichment. Against common benchmarks, DOCK Blaster recapitulates the crystal ligand pose within 2 Å rmsd 50−60% of the time; inferior to an expert, but respectrable. Half the time the ligand also ranked among the top 5% of 100 physically matched decoys chosen on the fly. Further tests were undertaken culminating in a study of 7755 eligible PDB structures. In 1398 cases, the redocked ligand ranked in the top 5% of 100 property-matched decoys while also posing within 2 Å rmsd, suggesting that unsupervised prospective docking is viable. DOCK Blaster is available at http://blaster.docking.org. PMID:19719084

Automated docking screens: a feasibility study.

PubMed

Irwin, John J; Shoichet, Brian K; Mysinger, Michael M; Huang, Niu; Colizzi, Francesco; Wassam, Pascal; Cao, Yiqun

2009-09-24

Molecular docking is the most practical approach to leverage protein structure for ligand discovery, but the technique retains important liabilities that make it challenging to deploy on a large scale. We have therefore created an expert system, DOCK Blaster, to investigate the feasibility of full automation. The method requires a PDB code, sometimes with a ligand structure, and from that alone can launch a full screen of large libraries. A critical feature is self-assessment, which estimates the anticipated reliability of the automated screening results using pose fidelity and enrichment. Against common benchmarks, DOCK Blaster recapitulates the crystal ligand pose within 2 A rmsd 50-60% of the time; inferior to an expert, but respectrable. Half the time the ligand also ranked among the top 5% of 100 physically matched decoys chosen on the fly. Further tests were undertaken culminating in a study of 7755 eligible PDB structures. In 1398 cases, the redocked ligand ranked in the top 5% of 100 property-matched decoys while also posing within 2 A rmsd, suggesting that unsupervised prospective docking is viable. DOCK Blaster is available at http://blaster.docking.org .

77 FR 50916 - Safety Zone; Boston Harbor's Rock Removal Project, Boston Inner Harbor, Boston, MA

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-23

... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket No. USCG-2012-0767] RIN 1625-AA00 Safety Zone; Boston Harbor's Rock Removal Project, Boston Inner Harbor, Boston, MA AGENCY: Coast.... 165.T01-0767 Safety Zone; Boston Harbor's Rock Removal Project, Boston Inner Harbor, Boston, MA. (a...

PTools: an opensource molecular docking library.

PubMed

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-05-01

Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.

Tales of some ancient harbors in the Aegean back-arc region: Earthquakes, coastal changes, historical impacts

NASA Astrophysics Data System (ADS)

Stiros, Stathis; Saltogianni, Vasso

2017-04-01

this ancient town since approximately AD200 as a result of loss of the only significant harbor along the southern coast of the Gulf of Corinth. Farther west, in the south part of the Greek mainland, rising of the level of the dock shortly after its construction may imply response to seismic land subsidence, while at the nearby harbor of Palairos, remains of a submerged breakwater, offset by several meters, testify to strike slip faulting with seismic offset amplified by liquefaction.

Expedition 39 Docking

NASA Image and Video Library

2014-03-28

A view of the Russian Mission Control Center in Korolev, Russia on Friday, March 28, 2014 prior to the docking of Soyuz TMA-12M. The Soyuz TMA-12M spacecraft docked to the International Space Station at 7:53 p.m. EDT bringing Expedition 39 Soyuz Commander Alexander Skvortsov of the Russian Federal Space Agency, Roscosmos, Flight Engineer Steve Swanson of NASA and Flight Engineer Oleg Artemyev of Roscosmos to the ISS for their six month stay aboard the orbiting labratory. Photo Credit: (NASA/Joel Kowsky)

33 CFR 125.15 - Access to waterfront facilities, and port and harbor areas, including vessels and harbor craft...

Code of Federal Regulations, 2010 CFR

2010-07-01

..., and port and harbor areas, including vessels and harbor craft therein. 125.15 Section 125.15....15 Access to waterfront facilities, and port and harbor areas, including vessels and harbor craft....09 to those waterfront facilities, and port and harbor areas, including vessels and harbor craft...

PTools: an opensource molecular docking library

PubMed Central

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-01-01

Background Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. Results We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. Conclusion The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation. PMID:19409097

NASA Docking System (NDS) Technical Integration Meeting

NASA Technical Reports Server (NTRS)

Lewis, James L.

2010-01-01

This slide presentation reviews the NASA Docking System (NDS) as NASA's implementation of the International Docking System Standard (IDSS). The goals of the NDS, is to build on proven technologies previously demonstrated in flight and to advance the state of the art of docking systems by incorporating Low Impact Docking System (LIDS) technology into the NDS. A Hardware Demonstration was included in the meeting, and there was discussion about software, NDS major system interfaces, integration information, schedule, and future upgrades.

Ground Demonstration on the Autonomous Docking of Two 3U CubeSats Using a Novel Permanent-Magnet Docking Mechanism

NASA Technical Reports Server (NTRS)

Pei, Jing; Murchison, Luke; BenShabat, Adam; Stewart, Victor; Rosenthal, James; Follman, Jacob; Branchy, Mark; Sellers, Drew; Elandt, Ryan; Elliott, Sawyer;

Magnet-Based System for Docking of Miniature Spacecraft

NASA Technical Reports Server (NTRS)

Howard, Nathan; Nguyen, Hai D.

2007-01-01

A prototype system for docking a miniature spacecraft with a larger spacecraft has been developed by engineers at the Johnson Space Center. Engineers working on Mini AERCam, a free-flying robotic camera, needed to find a way to successfully dock and undock their miniature spacecraft to refuel the propulsion and recharge the batteries. The subsystems developed (see figure) include (1) a docking port, designed for the larger spacecraft, which contains an electromagnet, a ball lock mechanism, and a service probe; and (2) a docking cluster, designed for the smaller spacecraft, which contains either a permanent magnet or an electromagnet. A typical docking operation begins with the docking spacecraft maneuvering into position near the docking port on the parent vehicle. The electromagnet( s) are then turned on, and, if necessary, the docking spacecraft is then maneuvered within the capture envelope of the docking port. The capture envelope for this system is approximated by a 5-in. (12.7-cm) cube centered on the front of the docking-port electromagnet and within an angular misalignment of <30 . Thereafter, the magnetic forces draw the smaller spacecraft toward the larger one and this brings the spacecraft into approximate alignment prior to contact. Mechanical alignment guides provide the final rotational alignment into one of 12 positions. Once the docking vehicle has been captured magnetically in the docking port, the ball-lock mechanism is activated, which locks the two spacecraft together. At this point the electromagnet( s) are turned off, and the service probe extended if recharge and refueling are to be performed. Additionally, during undocking, the polarity of one electromagnet can be reversed to provide a gentle push to separate the two spacecraft. This system is currently being incorporated into the design of Mini AERCam vehicle.

Suitlock Docking Mechanism

NASA Technical Reports Server (NTRS)

Culbertson, Philip, Jr. (Inventor)

1997-01-01

An environmental protective suit used for hazardous clean-up or space applications includes a suitlock docking mechanism that allows for easy egress and ingress of a crew member between a sealed vessel and a possibly contaminated environment. The suitlock docking mechanism comprises a single actuator that controls latches which, in turn, respectfully control rack and pinion assemblies that allow for easy removal and attachment of a life support equipment enclosure shell to the environmental protective suit or to the vehicle from which the operator performs his/her duties.

Voss with docking probe in Service module

NASA Image and Video Library

2001-05-30

ISS002-E-6478 (30 May 2001) --- James S. Voss, Expedition Two flight engineer, handles a spacecraft docking probe in the Service Module. The docking probe assists with the docking of the Soyuz and Progress vehicles to the International Space Station. The image was taken with a digital still camera.

Grounding of the Bahia Paraiso at Arthur Harbor, Antarctica. 1. Distribution and fate of oil spill related hydrocarbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kennicutt, M.C. II; Sweet, S.T.; Fraser, W.R.

1991-03-01

In January to March 1989 water, organisms, and sediments within a 2-mile radius of Arthur Harbor were contaminated with an estimated 600,000 L of petroleum spilled by the Bahia Paraiso. All components of the ecosystem were contaminated to varying degrees during the spill, including birds, limpets, macroalgae, clams, bottom-feeding fish, and sediments. The high-energy environment, the relatively small volume of material released, and the volatility of the released product all contributed to limiting toxic effects in time and space. The most effective removal processes were evaporation, dilution, winds, and currents. Sedimentation, biological uptake, microbial oxidation, and photooxidation accounted for removalmore » of only a minor portion of the spill. One year after the spill several areas still exhibited contamination. Subtidal sediments and the more distant intertidal locations were devoid of detectable PAH contaminants whereas sediments near the docking facility at Palmer Station continued to reflect localized nonspill-related activities in the area. Arthur Harbor and adjacent areas continue to be chronically exposed to low-level petroleum contamination emanating from the Bahia Paraiso.« less

New generation of docking programs: Supercomputer validation of force fields and quantum-chemical methods for docking.

PubMed

Sulimov, Alexey V; Kutov, Danil C; Katkova, Ekaterina V; Ilin, Ivan S; Sulimov, Vladimir B

2017-11-01

Discovery of new inhibitors of the protein associated with a given disease is the initial and most important stage of the whole process of the rational development of new pharmaceutical substances. New inhibitors block the active site of the target protein and the disease is cured. Computer-aided molecular modeling can considerably increase effectiveness of new inhibitors development. Reliable predictions of the target protein inhibition by a small molecule, ligand, is defined by the accuracy of docking programs. Such programs position a ligand in the target protein and estimate the protein-ligand binding energy. Positioning accuracy of modern docking programs is satisfactory. However, the accuracy of binding energy calculations is too low to predict good inhibitors. For effective application of docking programs to new inhibitors development the accuracy of binding energy calculations should be higher than 1kcal/mol. Reasons of limited accuracy of modern docking programs are discussed. One of the most important aspects limiting this accuracy is imperfection of protein-ligand energy calculations. Results of supercomputer validation of several force fields and quantum-chemical methods for docking are presented. The validation was performed by quasi-docking as follows. First, the low energy minima spectra of 16 protein-ligand complexes were found by exhaustive minima search in the MMFF94 force field. Second, energies of the lowest 8192 minima are recalculated with CHARMM force field and PM6-D3H4X and PM7 quantum-chemical methods for each complex. The analysis of minima energies reveals the docking positioning accuracies of the PM7 and PM6-D3H4X quantum-chemical methods and the CHARMM force field are close to one another and they are better than the positioning accuracy of the MMFF94 force field. Copyright © 2017 Elsevier Inc. All rights reserved.

Advanced Docking System With Magnetic Initial Capture

NASA Technical Reports Server (NTRS)

Lewis, James L.; Carroll, Monty B.; Morales, Ray; Le, Thang

2004-01-01

An advanced docking system is undergoing development to enable softer, safer docking than was possible when using prior docking systems. This system is intended for original use in docking of visiting spacecraft and berthing the Crew Return Vehicle at the International Space Station (ISS). The system could also be adapted to a variety of other uses in outer space and on Earth, including mating submersible vehicles, assembling structures, and robotic berthing/handling of payloads and cargo. Heretofore, two large spacecraft have been docked by causing the spacecraft to approach each other at a speed sufficient to activate capture latches - a procedure that results in large docking loads and is made more difficult because of the speed. The basic design and mode of operation of the present advanced docking system would eliminate the need to rely on speed of approach to activate capture latches, thereby making it possible to reduce approach speed and thus docking loads substantially. The system would comprise an active subsystem on one spacecraft and a passive subsystem on another spacecraft with which the active subsystem will be docked. The passive subsystem would include an extensible ring containing magnetic striker plates and guide petals. The active subsystem would include mating guide petals and electromagnets containing limit switches and would be arranged to mate with the magnetic striker plates and guide petals of the passive assembly. The electromagnets would be carried on (but not rigidly attached to) a structural ring that would be instrumented with load sensors. The outputs of the sensors would be sent, along with position information, as feedback to an electronic control subsystem. The system would also include electromechanical actuators that would extend or retract the ring upon command by the control subsystem.

Rendezvous and Docking for Space Exploration

NASA Technical Reports Server (NTRS)

Machula, M. F.; Crain, T.; Sandhoo, G. S.

2005-01-01

To achieve the exploration goals, new approaches to exploration are being envisioned that include robotic networks, modular systems, pre-positioned propellants and in-space assembly in Earth orbit, Lunar orbit and other locations around the cosmos. A fundamental requirement for rendezvous and docking to accomplish in-space assembly exists in each of these locations. While existing systems and technologies can accomplish rendezvous and docking in low earth orbit, and rendezvous and docking with crewed systems has been successfully accomplished in low lunar orbit, our capability must extend toward autonomous rendezvous and docking. To meet the needs of the exploration vision in-space assembly requiring both crewed and uncrewed vehicles will be an integral part of the exploration architecture. This paper focuses on the intelligent application of autonomous rendezvous and docking technologies to meet the needs of that architecture. It also describes key technology investments that will increase the exploration program's ability to ensure mission success, regardless of whether the rendezvous are fully automated or have humans in the loop.

POSE Algorithms for Automated Docking

NASA Technical Reports Server (NTRS)

Heaton, Andrew F.; Howard, Richard T.

2011-01-01

POSE (relative position and attitude) can be computed in many different ways. Given a sensor that measures bearing to a finite number of spots corresponding to known features (such as a target) of a spacecraft, a number of different algorithms can be used to compute the POSE. NASA has sponsored the development of a flash LIDAR proximity sensor called the Vision Navigation Sensor (VNS) for use by the Orion capsule in future docking missions. This sensor generates data that can be used by a variety of algorithms to compute POSE solutions inside of 15 meters, including at the critical docking range of approximately 1-2 meters. Previously NASA participated in a DARPA program called Orbital Express that achieved the first automated docking for the American space program. During this mission a large set of high quality mated sensor data was obtained at what is essentially the docking distance. This data set is perhaps the most accurate truth data in existence for docking proximity sensors in orbit. In this paper, the flight data from Orbital Express is used to test POSE algorithms at 1.22 meters range. Two different POSE algorithms are tested for two different Fields-of-View (FOVs) and two different pixel noise levels. The results of the analysis are used to predict future performance of the POSE algorithms with VNS data.

Proximity Operations and Docking Sensor Development

NASA Technical Reports Server (NTRS)

Howard, Richard T.; Bryan, Thomas C.; Brewster, Linda L.; Lee, James E.

2009-01-01

The Next Generation Advanced Video Guidance Sensor (NGAVGS) has been under development for the last three years as a long-range proximity operations and docking sensor for use in an Automated Rendezvous and Docking (AR&D) system. The first autonomous rendezvous and docking in the history of the U.S. Space Program was successfully accomplished by Orbital Express, using the Advanced Video Guidance Sensor (AVGS) as the primary docking sensor. That flight proved that the United States now has a mature and flight proven sensor technology for supporting Crew Exploration Vehicles (CEV) and Commercial Orbital Transport Systems (COTS) Automated Rendezvous and Docking (AR&D). NASA video sensors have worked well in the past: the AVGS used on the Demonstration of Autonomous Rendezvous Technology (DART) mission operated successfully in spot mode out to 2 km, and the first generation rendezvous and docking sensor, the Video Guidance Sensor (VGS), was developed and successfully flown on Space Shuttle flights in 1997 and 1998. 12 Parts obsolescence issues prevent the construction of more AVGS units, and the next generation sensor was updated to allow it to support the CEV and COTS programs. The flight proven AR&D sensor has been redesigned to update parts and add additional capabilities for CEV and COTS with the development of the Next Generation AVGS at the Marshall Space Flight Center. The obsolete imager and processor are being replaced with new radiation tolerant parts. In addition, new capabilities include greater sensor range, auto ranging capability, and real-time video output. This paper presents some sensor hardware trades, use of highly integrated laser components, and addresses the needs of future vehicles that may rendezvous and dock with the International Space Station (ISS) and other Constellation vehicles. It also discusses approaches for upgrading AVGS to address parts obsolescence, and concepts for minimizing the sensor footprint, weight, and power requirements

Text Mining for Protein Docking

PubMed Central

Badal, Varsha D.; Kundrotas, Petras J.; Vakser, Ilya A.

2015-01-01

The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking). Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu). The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features) approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound benchmark set

ATV 2 Johannes Kepler docked

NASA Image and Video Library

2011-02-24

ISS026-E-029294 (24 Feb. 2011) --- Backdropped by the blackness of space, the European Space Agency's "Johannes Kepler" Automated Transfer Vehicle-2 (ATV-2) docks to the aft end of the International Space Station's Zvezda Service Module. Docking of the two spacecraft occurred at 10:59 a.m. (EST) on Feb. 24, 2011.

Autonomous docking ground demonstration

NASA Technical Reports Server (NTRS)

Lamkin, Steve L.; Le, Thomas Quan; Othon, L. T.; Prather, Joseph L.; Eick, Richard E.; Baxter, Jim M.; Boyd, M. G.; Clark, Fred D.; Spehar, Peter T.; Teters, Rebecca T.

1991-01-01

The Autonomous Docking Ground Demonstration is an evaluation of the laser sensor system to support the docking phase (12 ft to contact) when operated in conjunction with the guidance, navigation, and control (GN&C) software. The docking mechanism being used was developed for the Apollo/Soyuz Test Program. This demonstration will be conducted using the 6-DOF Dynamic Test System (DTS). The DTS simulates the Space Station Freedom as the stationary or target vehicle and the Orbiter as the active or chase vehicle. For this demonstration, the laser sensor will be mounted on the target vehicle and the retroflectors will be on the chase vehicle. This arrangement was chosen to prevent potential damage to the laser. The laser sensor system, GN&C, and 6-DOF DTS will be operated closed-loop. Initial conditions to simulate vehicle misalignments, translational and rotational, will be introduced within the constraints of the systems involved.

Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2

NASA Astrophysics Data System (ADS)

Salmaso, Veronica; Sturlese, Mattia; Cuzzolin, Alberto; Moro, Stefano

2018-01-01

Molecular docking is a powerful tool in the field of computer-aided molecular design. In particular, it is the technique of choice for the prediction of a ligand pose within its target binding site. A multitude of docking methods is available nowadays, whose performance may vary depending on the data set. Therefore, some non-trivial choices should be made before starting a docking simulation. In the same framework, the selection of the target structure to use could be challenging, since the number of available experimental structures is increasing. Both issues have been explored within this work. The pose prediction of a pool of 36 compounds provided by D3R Grand Challenge 2 organizers was preceded by a pipeline to choose the best protein/docking-method couple for each blind ligand. An integrated benchmark approach including ligand shape comparison and cross-docking evaluations was implemented inside our DockBench software. The results are encouraging and show that bringing attention to the choice of the docking simulation fundamental components improves the results of the binding mode predictions.

Expedition 19 Docks to ISS

NASA Image and Video Library

2009-03-27

Russian Orthodox Priest, Vladyka Feofan speaks during a Soyuz post-docking press conference at the Russian mission Control Center in Korolev, Russia on Saturday March 28, 2009. The Soyuz TMA-14 docked to the International Space Station carrying Expedition 19 Commander Gennady I. Padalka, Flight Engineer Michael R. Barratt and Spaceflight Participant Charles Simonyi. Photo Credit: (NASA/Bill Ingalls)

High performance transcription factor-DNA docking with GPU computing

PubMed Central

2012-01-01

Background Protein-DNA docking is a very challenging problem in structural bioinformatics and has important implications in a number of applications, such as structure-based prediction of transcription factor binding sites and rational drug design. Protein-DNA docking is very computational demanding due to the high cost of energy calculation and the statistical nature of conformational sampling algorithms. More importantly, experiments show that the docking quality depends on the coverage of the conformational sampling space. It is therefore desirable to accelerate the computation of the docking algorithm, not only to reduce computing time, but also to improve docking quality. Methods In an attempt to accelerate the sampling process and to improve the docking performance, we developed a graphics processing unit (GPU)-based protein-DNA docking algorithm. The algorithm employs a potential-based energy function to describe the binding affinity of a protein-DNA pair, and integrates Monte-Carlo simulation and a simulated annealing method to search through the conformational space. Algorithmic techniques were developed to improve the computation efficiency and scalability on GPU-based high performance computing systems. Results The effectiveness of our approach is tested on a non-redundant set of 75 TF-DNA complexes and a newly developed TF-DNA docking benchmark. We demonstrated that the GPU-based docking algorithm can significantly accelerate the simulation process and thereby improving the chance of finding near-native TF-DNA complex structures. This study also suggests that further improvement in protein-DNA docking research would require efforts from two integral aspects: improvement in computation efficiency and energy function design. Conclusions We present a high performance computing approach for improving the prediction accuracy of protein-DNA docking. The GPU-based docking algorithm accelerates the search of the conformational space and thus increases the

Ligand- and receptor-based docking with LiBELa

NASA Astrophysics Data System (ADS)

dos Santos Muniz, Heloisa; Nascimento, Alessandro S.

2015-08-01

Methodologies on molecular docking are constantly improving. The problem consists on finding an optimal interplay between the computational cost and a satisfactory physical description of ligand-receptor interaction. In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placement of the docking molecule and an interaction energy-based global minimization follows. This hybrid docking was evaluated with soft-core and force field potentials taking into account ligand pose and scoring. Our approach was found to be competitive to a purely receptor-based dock resulting in improved logAUC values when evaluated with DUD and DUD-E. Furthermore, the smoothed potential as evaluated here, was not advantageous when ligand binding poses were compared to experimentally determined conformations. In conclusion we show that a combination of ligand- and receptor-based strategy docking with a force field energy model results in good reproduction of binding poses and enrichment of active molecules against decoys. This strategy is implemented in our tool, LiBELa, available to the scientific community.

American & Soviet engineers examine ASTP docking set-up following tests

NASA Image and Video Library

1974-07-10

S74-25394 (10 July 1974) --- A group of American and Soviet engineers of the Apollo-Soyuz Test Project working group three examines an ASTP docking set-up following a docking mechanism fitness test conducted in Building 13 at the Johnson Space Center. Working Group No. 3 is concerned with ASTP docking problems and techniques. The joint U.S.-USSR ASTP docking mission in Earth orbit is scheduled for the summer of 1975. The Apollo docking mechanism is atop the Soyuz docking mechanism.

A measurement of summertime dry deposition of ambient air particulates and associated metallic pollutants in Central Taiwan.

PubMed

Fang, Guor-Cheng; Chiang, Hung-Che; Chen, Yu-Cheng; Xiao, You-Fu; Wu, Chia-Ming; Kuo, Yu-Chen

2015-04-01

The purpose of this study is to characterize metallic elements associated with atmospheric particulate matter in the dry deposition plate, total suspended particulate, fine particles, and coarse particles at Taichung Harbor and Gong Ming Junior High School (airport) in central Taiwan at a sampling site from June 2013 to August 2013. The results indicated that: (1) the average concentrations of the metallic elements Cr and Cd were highest at the Gong Ming Junior High School (airport), and the average concentrations of the metallic elements Ni, Cu, and Pb were highest at the Taichung Harbor sampling site. (2) The high smelting industry density and export/import rate of heavily loaded cargos were the main reasons leading to these findings. (3) The average metallic element dry deposition and metallic element PM(2.5-10) all followed the order of Pb > Cr > Cu > Ni > Cd at the two sampling sites. However, the average metallic elements Cu and Pb were found to have the highest dry deposition velocities and concentrations in PM(2.5) for the two sampling sites in this study. (4) The correlation coefficients of ambient air particle dry deposition and concentration with wind speed at the airport were higher than those from the harbor sampling site. The wind and broad open spaces at Taichung Airport were the possible reasons for the increasing correlation coefficients for ambient air particle concentration and dry deposition with wind speed at the Taichung Airport sampling site.

Lessons in molecular recognition. 2. Assessing and improving cross-docking accuracy.

PubMed

Sutherland, Jeffrey J; Nandigam, Ravi K; Erickson, Jon A; Vieth, Michal

2007-01-01

Docking methods are used to predict the manner in which a ligand binds to a protein receptor. Many studies have assessed the success rate of programs in self-docking tests, whereby a ligand is docked into the protein structure from which it was extracted. Cross-docking, or using a protein structure from a complex containing a different ligand, provides a more realistic assessment of a docking program's ability to reproduce X-ray results. In this work, cross-docking was performed with CDocker, Fred, and Rocs using multiple X-ray structures for eight proteins (two kinases, one nuclear hormone receptor, one serine protease, two metalloproteases, and two phosphodiesterases). While average cross-docking accuracy is not encouraging, it is shown that using the protein structure from the complex that contains the bound ligand most similar to the docked ligand increases docking accuracy for all methods ("similarity selection"). Identifying the most successful protein conformer ("best selection") and similarity selection substantially reduce the difference between self-docking and average cross-docking accuracy. We identify universal predictors of docking accuracy (i.e., showing consistent behavior across most protein-method combinations), and show that models for predicting docking accuracy built using these parameters can be used to select the most appropriate docking method.

Expedition 19 Docks to ISS

NASA Image and Video Library

2009-03-27

Vladimir Solovyov, Chief Flight Director, MCC-M, answers reporters questions during a Soyuz post-docking press conference at the Russian mission Control Center in Korolev, Russia on Saturday March 28, 2009. The Soyuz TMA-14 docked to the International Space Station carrying Expedition 19 Commander Gennady I. Padalka, Flight Engineer Michael R. Barratt and Spaceflight Participant Charles Simonyi. Photo Credit: (NASA/Bill Ingalls)

Expedition 19 Docks to ISS

NASA Image and Video Library

2009-03-27

Vitaly Lopota, President, General Designer, RSC-Energia, answers reporters questions during a Soyuz post-docking press conference at the Russian mission Control Center in Korolev, Russia on Saturday March 28, 2009. The Soyuz TMA-14 docked to the International Space Station carrying Expedition 19 Commander Gennady I. Padalka, Flight Engineer Michael R. Barratt and Spaceflight Participant Charles Simonyi. Photo Credit: (NASA/Bill Ingalls)

Investigation of MM-PBSA rescoring of docking poses.

PubMed

Thompson, David C; Humblet, Christine; Joseph-McCarthy, Diane

2008-05-01

Target-based virtual screening is increasingly used to generate leads for targets for which high quality three-dimensional (3D) structures are available. To allow large molecular databases to be screened rapidly, a tiered scoring scheme is often employed whereby a simple scoring function is used as a fast filter of the entire database and a more rigorous and time-consuming scoring function is used to rescore the top hits to produce the final list of ranked compounds. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approaches are currently thought to be quite effective at incorporating implicit solvation into the estimation of ligand binding free energies. In this paper, the ability of a high-throughput MM-PBSA rescoring function to discriminate between correct and incorrect docking poses is investigated in detail. Various initial scoring functions are used to generate docked poses for a subset of the CCDC/Astex test set and to dock one set of actives/inactives from the DUD data set. The effectiveness of each of these initial scoring functions is discussed. Overall, the ability of the MM-PBSA rescoring function to (i) regenerate the set of X-ray complexes when docking the bound conformation of the ligand, (ii) regenerate the X-ray complexes when docking conformationally expanded databases for each ligand which include "conformation decoys" of the ligand, and (iii) enrich known actives in a virtual screen for the mineralocorticoid receptor in the presence of "ligand decoys" is assessed. While a pharmacophore-based molecular docking approach, PhDock, is used to carry out the docking, the results are expected to be general to use with any docking method.

Development of robotics facility docking test hardware

NASA Technical Reports Server (NTRS)

Loughead, T. E.; Winkler, R. V.

1984-01-01

Design and fabricate test hardware for NASA's George C. Marshall Space Flight Center (MSFC) are reported. A docking device conceptually developed was fabricated, and two docking targets which provide high and low mass docking loads were required and were represented by an aft 61.0 cm section of a Hubble space telescope (ST) mockup and an upgrading of an existing multimission modular spacecraft (MSS) mockup respectively. A test plan is developed for testing the hardware.

Orbital docking system centerline color television camera system test

NASA Technical Reports Server (NTRS)

Mongan, Philip T.

1993-01-01

A series of tests was run to verify that the design of the centerline color television camera (CTVC) system is adequate optically for the STS-71 Space Shuttle Orbiter docking mission with the Mir space station. In each test, a mockup of the Mir consisting of hatch, docking mechanism, and docking target was positioned above the Johnson Space Center's full fuselage trainer, which simulated the Orbiter with a mockup of the external airlock and docking adapter. Test subjects viewed the docking target through the CTVC under 30 different lighting conditions and evaluated target resolution, field of view, light levels, light placement, and methods of target alignment. Test results indicate that the proposed design will provide adequate visibility through the centerline camera for a successful docking, even with a reasonable number of light failures. It is recommended that the flight deck crew have individual switching capability for docking lights to provide maximum shadow management and that centerline lights be retained to deal with light failures and user preferences. Procedures for light management should be developed and target alignment aids should be selected during simulated docking runs.

Kotov in SM during Progress 37P Docking

NASA Image and Video Library

2010-05-01

ISS023-E-031743 (1 May 2010) --- Russian cosmonaut Oleg Kotov, Expedition 23 commander, is pictured at the manual TORU docking system controls in the Zvezda Service Module of the International Space Station just before conducting a manual control docking of the Progress 37 due to a jet failure on the Progress that forced a shutdown of the Kurs automated rendezvous system. Progress 37 docked to the Pirs Docking Compartment at 2:30 p.m. (EDT) on May 1, 2010, after a three-day flight from the Baikonur Cosmodrome in Kazakhstan.

DOCKSCORE: a webserver for ranking protein-protein docked poses.

PubMed

Malhotra, Sony; Mathew, Oommen K; Sowdhamini, Ramanathan

2015-04-24

Proteins interact with a variety of other molecules such as nucleic acids, small molecules and other proteins inside the cell. Structure-determination of protein-protein complexes is challenging due to several reasons such as the large molecular weights of these macromolecular complexes, their dynamic nature, difficulty in purification and sample preparation. Computational docking permits an early understanding of the feasibility and mode of protein-protein interactions. However, docking algorithms propose a number of solutions and it is a challenging task to select the native or near native pose(s) from this pool. DockScore is an objective scoring scheme that can be used to rank protein-protein docked poses. It considers several interface parameters, namely, surface area, evolutionary conservation, hydrophobicity, short contacts and spatial clustering at the interface for scoring. We have implemented DockScore in form of a webserver for its use by the scientific community. DockScore webserver can be employed, subsequent to docking, to perform scoring of the docked solutions, starting from multiple poses as inputs. The results, on scores and ranks for all the poses, can be downloaded as a csv file and graphical view of the interface of best ranking poses is possible. The webserver for DockScore is made freely available for the scientific community at: http://caps.ncbs.res.in/dockscore/ .

Expedition 19 Docks to ISS

NASA Image and Video Library

2009-03-27

Alexei Krasnov, Director of Manned Space Programs Department, Roscosmos, answers reporters questions during a Soyuz post-docking press conference at the Russian mission Control Center in Korolev, Russia on Saturday March 28, 2009. The Soyuz TMA-14 docked to the International Space Station carrying Expedition 19 Commander Gennady I. Padalka, Flight Engineer Michael R. Barratt and Spaceflight Participant Charles Simonyi. Photo Credit: (NASA/Bill Ingalls)

Expedition 19 Docks to ISS

NASA Image and Video Library

2009-03-27

Managers from NASA, Roscosmos, RSC-Energia and other related agencies answer reporters questions during a Soyuz post-docking press conference at the Russian mission Control Center in Korolev, Russia on Saturday March 28, 2009. The Soyuz TMA-14 docked to the International Space Station carrying Expedition 19 Commander Gennady I. Padalka, Flight Engineer Michael R. Barratt and Spaceflight Participant Charles Simonyi. Photo Credit: (NASA/Bill Ingalls)

PaFlexPepDock: parallel ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta.

PubMed

Li, Haiou; Lu, Liyao; Chen, Rong; Quan, Lijun; Xia, Xiaoyan; Lü, Qiang

2014-01-01

Structural information related to protein-peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein-peptide interactions explored by experimental ways. Protein-peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide folding, peptide docking with its receptor, and refinement of some flexible areas of the receptor as the peptide is approaching. Several existing methods have been used to sample the degrees of freedom in the three processes, which are usually triggered in an organized sequential scheme. In this paper, we proposed a parallel approach that combines all the three processes during the docking of a folding peptide with a flexible receptor. This approach mimics the actual protein-peptide docking process in parallel way, and is expected to deliver better performance than sequential approaches. We used 22 unbound protein-peptide docking examples to evaluate our method. Our analysis of the results showed that the explicit refinement of the flexible areas of the receptor facilitated more accurate modeling of the interfaces of the complexes, while combining all of the moves in parallel helped the constructing of energy funnels for predictions.

Orion Handling Qualities During ISS Rendezvous and Docking

NASA Technical Reports Server (NTRS)

Hart, Jeremy J.; Stephens, J. P.; Spehar, P.; Bilimoria, K.; Foster, C.; Gonzalex, R.; Sullivan, K.; Jackson, B.; Brazzel, J.; Hart, J.

2011-01-01

The Orion spacecraft was designed to rendezvous with multiple vehicles in low earth orbit (LEO) and beyond. To perform the required rendezvous and docking task, Orion must provide enough control authority to perform coarse translational maneuvers while maintaining precision to perform the delicate docking corrections. While Orion has autonomous docking capabilities, it is expected that final approach and docking operations with the International Space Station (ISS) will initially be performed in a manual mode. A series of evaluations was conducted by NASA and Lockheed Martin at the Johnson Space Center to determine the handling qualities (HQ) of the Orion spacecraft during different docking and rendezvous conditions using the Cooper-Harper scale. This paper will address the specifics of the handling qualities methodology, vehicle configuration, scenarios flown, data collection tools, and subject ratings and comments. The initial Orion HQ assessment examined Orion docking to the ISS. This scenario demonstrates the Translational Hand Controller (THC) handling qualities of Orion. During this initial assessment, two different scenarios were evaluated. The first was a nominal docking approach to a stable ISS, with Orion initializing with relative position dispersions and a closing rate of approximately 0.1 ft/sec. The second docking scenario was identical to the first, except the attitude motion of the ISS was modeled to simulate a stress case ( 1 degree deadband per axis and 0.01 deg/sec rate deadband per axis). For both scenarios, subjects started each run on final approach at a docking port-to-port range of 20 ft. Subjects used the THC in pulse mode with cues from the docking camera image, window views, and range and range rate data displayed on the Orion display units. As in the actual design, the attitude of the Orion vehicle was held by the automated flight control system at 0.5 degree deadband per axis. Several error sources were modeled including Reaction

Kotov practices the manual docking techniques with the TORU

NASA Image and Video Library

2013-11-22

ISS038-E-006656 (22 Nov. 2013) --- Russian cosmonaut Oleg Kotov, Expedition 38 commander, practices manual docking techniques with the TORU, or telerobotically operated rendezvous system, in the Zvezda Service Module of the International Space Station in preparation for the docking of the Progress 53 spacecraft. Kotov, using the Simvol-TS screen and hand controllers, could manually dock the Progress to the station in the event of a failure of the Kurs automated docking system. The Progress 53 craft is scheduled to complete its automated docking to the aft port of Zvezda at 5:28 p.m. (EST) on Nov. 29.

Tyurin practices the manual docking techniques with the TORU

NASA Image and Video Library

2013-11-22

ISS038-E-006663 (22 Nov. 2013) --- Russian cosmonaut Mikhail Tyurin, Expedition 38 flight engineer, practices manual docking techniques with the TORU, or telerobotically operated rendezvous system, in the Zvezda Service Module of the International Space Station in preparation for the docking of the Progress 53 spacecraft. Tyurin, using the Simvol-TS screen and hand controllers, could manually dock the Progress to the station in the event of a failure of the Kurs automated docking system. The Progress 53 craft is scheduled to complete its automated docking to the aft port of Zvezda at 5:28 p.m. (EST) on Nov. 29.

Apollo Docking with the LEM Target

NASA Image and Video Library

2012-09-07

Originally the Rendezvous was used by the astronauts preparing for Gemini missions. The Rendezvous Docking Simulator was then modified and used to develop docking techniques for the Apollo program. This picture shows a later configuration of the Apollo docking with the LEM target. A.W. Vogeley described the simulator as follows: The Rendezvous Docking Simulator and also the Lunar Landing Research Facility are both rather large moving-base simulators. It should be noted, however, that neither was built primarily because of its motion characteristics. The main reason they were built was to provide a realistic visual scene. A secondary reason was that they would provide correct angular motion cues (important in control of vehicle short-period motions) even though the linear acceleration cues would be incorrect. -- Published in A.W. Vogeley, Piloted Space-Flight Simulation at Langley Research Center, Paper presented at the American Society of Mechanical Engineers, 1966 Winter Meeting, New York, NY, November 27 - December 1, 1966.

A Comparison of Candidate Seal Designs for Future Docking Systems

NASA Technical Reports Server (NTRS)

Dunlap, Patrick, H., Jr.; Steinetz, Bruce, M.

2012-01-01

NASA is developing a new docking system to support future space exploration missions to low Earth orbit, the Moon, and other destinations. A key component of this system is the seal at the main docking interface which inhibits the loss of cabin air once docking is complete. Depending on the mission, the seal must be able to dock in either a seal-on-flange or seal-on-seal configuration. Seal-on-flange mating would occur when a docking system equipped with a seal docks to a system with a flat metal flange. This would occur when a vehicle docks to a node on the International Space Station. Seal-on-seal mating would occur when two docking systems equipped with seals dock to each other. Two types of seal designs were identified for this application: Gask-O-seals and multi-piece seals. Both types of seals had a pair of seal bulbs to satisfy the redundancy requirement. A series of performance assessments and comparisons were made between the candidate seal designs indicating that they meet the requirements for leak rate and compression and adhesion loads under a range of operating conditions. Other design factors such as part count, integration into the docking system tunnel, seal-on-seal mating, and cost were also considered leading to the selection of the multi-piece seal design for the new docking system. The results of this study can be used by designers of future docking systems and other habitable volumes to select the seal design best-suited for their particular application.

SnapDock—template-based docking by Geometric Hashing

PubMed Central

Estrin, Michael; Wolfson, Haim J.

2017-01-01

Abstract Motivation: A highly efficient template-based protein–protein docking algorithm, nicknamed SnapDock, is presented. It employs a Geometric Hashing-based structural alignment scheme to align the target proteins to the interfaces of non-redundant protein–protein interface libraries. Docking of a pair of proteins utilizing the 22 600 interface PIFACE library is performed in < 2 min on the average. A flexible version of the algorithm allowing hinge motion in one of the proteins is presented as well. Results: To evaluate the performance of the algorithm a blind re-modelling of 3547 PDB complexes, which have been uploaded after the PIFACE publication has been performed with success ratio of about 35%. Interestingly, a similar experiment with the template free PatchDock docking algorithm yielded a success rate of about 23% with roughly 1/3 of the solutions different from those of SnapDock. Consequently, the combination of the two methods gave a 42% success ratio. Availability and implementation: A web server of the application is under development. Contact: michaelestrin@gmail.com or wolfson@tau.ac.il PMID:28881968

Six degree of freedom FORTRAN program, ASTP docking dynamics, users guide

NASA Technical Reports Server (NTRS)

Mount, G. O., Jr.; Mikhalkin, B.

1974-01-01

The digital program ASTP Docking Dynamics as outlined is intended to aid the engineer using the program to determine the docking system loads and attendant vehicular motion resulting from docking two vehicles that have an androgynous, six-hydraulic-attenuator, guide ring, docking interface similar to that designed for the Apollo/Soyuz Test Project (ASTP). This program is set up to analyze two different vehicle combinations: the Apollo CSM docking to Soyuz and the shuttle orbiter docking to another orbiter. The subroutine modifies the vehicle control systems to describe one or the other vehicle combinations; the rest of the vehicle characteristics are changed by input data. To date, the program has been used to predict and correlate ASTP docking loads and performance with docking test program results from dynamic testing. The program modified for use on IBM 360 computers. Parts of the original docking system equations in the areas of hydraulic damping and capture latches are modified to better describe the detail design of the ASTP docking system.

Modeling and docking antibody structures with Rosetta

PubMed Central

Weitzner, Brian D.; Jeliazkov, Jeliazko R.; Lyskov, Sergey; Marze, Nicholas; Kuroda, Daisuke; Frick, Rahel; Adolf-Bryfogle, Jared; Biswas, Naireeta; Dunbrack, Roland L.; Gray, Jeffrey J.

2017-01-01

We describe Rosetta-based computational protocols for predicting the three-dimensional structure of an antibody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (SnugDock). Antibody modeling leverages canonical loop conformations to graft large segments from experimentally-determined structures as well as (1) energetic calculations to minimize loops, (2) docking methodology to refine the VL–VH relative orientation, and (3) de novo prediction of the elusive complementarity determining region (CDR) H3 loop. To alleviate model uncertainty, antibody–antigen docking resamples CDR loop conformations and can use multiple models to represent an ensemble of conformations for the antibody, the antigen or both. These protocols can be run fully-automated via the ROSIE web server (http://rosie.rosettacommons.org/) or manually on a computer with user control of individual steps. For best results, the protocol requires roughly 1,000 CPU-hours for antibody modeling and 250 CPU-hours for antibody–antigen docking. Tasks can be completed in under a day by using public supercomputers. PMID:28125104

1. Full SW side of dock as viewed from shore ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. Full SW side of dock as viewed from shore at the Oil/Creosote Unloading Dock. This view formed a panorama with photo WA-131-H-5, which shows the Oil/Creosote Unloading Dock. - Pacific Creosoting Plant, West Dock, 5350 Creosote Place, Northeast, Bremerton, Kitsap County, WA

Expedition 19 Docks to ISS

NASA Image and Video Library

2009-03-27

Managers from NASA, Roscosmos, RSC-Energia, TsNIIMash and other related agencies answer reporters questions during a Soyuz post-docking press conference at the Russian mission Control Center in Korolev, Russia on Saturday March 28, 2009. The Soyuz TMA-14 docked to the International Space Station carrying Expedition 19 Commander Gennady I. Padalka, Flight Engineer Michael R. Barratt and Spaceflight Participant Charles Simonyi. Photo Credit: (NASA/Bill Ingalls)

Improved Ball-and-Socket Docking Mechanism

NASA Technical Reports Server (NTRS)

Cloyd, Richard; Bryan, Tom

2004-01-01

A proposed docking mechanism would form a ball-and-socket joint in the docked condition. The mechanism could tolerate significant initial misalignment because it would include an alignment cone that would guide the ball into the socket. Like other ball-and-socket joints, the joint would have three rotational degrees of freedom. This docking mechanism would be a successor to the one described in Passive Capture Joint With Three Degrees of Freedom (MFS-31146), NASA Tech Briefs, Vol. 22, No. 7 (July 1998), page 65. It would contain most of the components of the prior mechanism, plus some additional components that would expand its capabilities.

Electro-optical rendezvous and docking sensors

NASA Technical Reports Server (NTRS)

Tubbs, David J.; Kesler, Lynn O.; Sirko, Robert J.

1991-01-01

Electro-optical sensors provide unique and critical functionality for space missions requiring rendezvous, docking, and berthing. McDonnell Douglas is developing a complete rendezvous and docking system for both manned and unmanned missions. This paper examines our sensor development and the systems and missions which benefit from rendezvous and docking sensors. Simulation results quantifying system performance improvements in key areas are given, with associated sensor performance requirements. A brief review of NASA-funded development activities and the current performance of electro-optical sensors for space applications is given. We will also describe current activities at McDonnell Douglas for a fully functional demonstration to address specific NASA mission needs.

Docking screens: right for the right reasons?

PubMed

Kolb, Peter; Irwin, John J

2009-01-01

Whereas docking screens have emerged as the most practical way to use protein structure for ligand discovery, an inconsistent track record raises questions about how well docking actually works. In its favor, a growing number of publications report the successful discovery of new ligands, often supported by experimental affinity data and controls for artifacts. Few reports, however, actually test the underlying structural hypotheses that docking makes. To be successful and not just lucky, prospective docking must not only rank a true ligand among the top scoring compounds, it must also correctly orient the ligand so the score it receives is biophysically sound. If the correct binding pose is not predicted, a skeptic might well infer that the discovery was serendipitous. Surveying over 15 years of the docking literature, we were surprised to discover how rarely sufficient evidence is presented to establish whether docking actually worked for the right reasons. The paucity of experimental tests of theoretically predicted poses undermines confidence in a technique that has otherwise become widely accepted. Of course, solving a crystal structure is not always possible, and even when it is, it can be a lot of work, and is not readily accessible to all groups. Even when a structure can be determined, investigators may prefer to gloss over an erroneous structural prediction to better focus on their discovery. Still, the absence of a direct test of theory by experiment is a loss for method developers seeking to understand and improve docking methods. We hope this review will motivate investigators to solve structures and compare them with their predictions whenever possible, to advance the field.

33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Harbor, to the northwest point. (b) Effective times and dates. This safety and security zone will be in... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone...

Gemini Rendezvous Docking Simulator

NASA Image and Video Library

1964-05-11

Gemini Rendezvous Docking Simulator suspended from the roof of the Langley Research Center s aircraft hangar. Francis B. Smith wrote: The rendezvous and docking operation of the Gemini spacecraft with the Agena and of the Apollo Command Module with the Lunar Excursion Module have been the subject of simulator studies for several years. This figure illustrates the Gemini-Agena rendezvous docking simulator at Langley. The Gemini spacecraft was supported in a gimbal system by an overhead crane and gantry arrangement which provided 6 degrees of freedom - roll, pitch, yaw, and translation in any direction - all controllable by the astronaut in the spacecraft. Here again the controls fed into a computer which in turn provided an input to the servos driving the spacecraft so that it responded to control motions in a manner which accurately simulated the Gemini spacecraft. -- Published in Barton C. Hacker and James M. Grimwood, On the Shoulders of Titans: A History of Project Gemini, NASA SP-4203 Francis B. Smith, Simulators for Manned Space Research, Paper presented at the 1966 IEEE International convention, March 21-25, 1966.

"Soft docking": matching of molecular surface cubes.

PubMed

Jiang, F; Kim, S H

1991-05-05

Molecular recognition is achieved through the complementarity of molecular surface structures and energetics with, most commonly, associated minor conformational changes. This complementarity can take many forms: charge-charge interaction, hydrogen bonding, van der Waals' interaction, and the size and shape of surfaces. We describe a method that exploits these features to predict the sites of interactions between two cognate molecules given their three-dimensional structures. We have developed a "cube representation" of molecular surface and volume which enables us not only to design a simple algorithm for a six-dimensional search but also to allow implicitly the effects of the conformational changes caused by complex formation. The present molecular docking procedure may be divided into two stages. The first is the selection of a population of complexes by geometric "soft docking", in which surface structures of two interacting molecules are matched with each other, allowing minor conformational changes implicitly, on the basis of complementarity in size and shape, close packing, and the absence of steric hindrance. The second is a screening process to identify a subpopulation with many favorable energetic interactions between the buried surface areas. Once the size of the subpopulation is small, one may further screen to find the correct complex based on other criteria or constraints obtained from biochemical, genetic, and theoretical studies, including visual inspection. We have tested the present method in two ways. First is a control test in which we docked the components of a molecular complex of known crystal structure available in the Protein Data Bank (PDB). Two molecular complexes were used: (1) a ternary complex of dihydrofolate reductase, NADPH and methotrexate (3DFR in PDB) and (2) a binary complex of trypsin and trypsin inhibitor (2PTC in PDB). The components of each complex were taken apart at an arbitrary relative orientation and then docked

Boom Rendezvous Alternative Docking Approach

NASA Technical Reports Server (NTRS)

Bonometti, Joseph A.

2006-01-01

Space rendezvous and docking has always been attempted with primarily one philosophic methodology. The slow matching of one vehicle's orbit by a second vehicle and then a final closing sequence that ends in matching the orbits with perfect precision and with near zero relative velocities. The task is time consuming, propellant intensive, risk inherent (plume impingement, collisions, fuel depletion, etc.) and requires substantial hardware mass. The historical background and rationale as to why this approach is used is discussed in terms of the path-not-taken and in light of an alternate methodology. Rendezvous and docking by boom extension is suggested to have inherent advantages that today s technology can readily exploit. Extension from the primary spacecraft, beyond its inherent large inertia, allows low inertia connections to be made rapidly and safely. Plume contamination issues are eliminated as well as the extra propellant mass and risk required for the final thruster (docking) operations. Space vehicle connection hardware can be significantly lightened. Also, docking sensors and controls require less fidelity; allowing them to be more robust and less sensitive. It is the potential safety advantage and mission risk reduction that makes this approach attractive, besides the prospect of nominal time and mass savings.

Autonomous spacecraft rendezvous and docking

NASA Technical Reports Server (NTRS)

Tietz, J. C.; Almand, B. J.

1985-01-01

A storyboard display is presented which summarizes work done recently in design and simulation of autonomous video rendezvous and docking systems for spacecraft. This display includes: photographs of the simulation hardware, plots of chase vehicle trajectories from simulations, pictures of the docking aid including image processing interpretations, and drawings of the control system strategy. Viewgraph-style sheets on the display bulletin board summarize the simulation objectives, benefits, special considerations, approach, and results.

Autonomous spacecraft rendezvous and docking

NASA Astrophysics Data System (ADS)

Tietz, J. C.; Almand, B. J.

A storyboard display is presented which summarizes work done recently in design and simulation of autonomous video rendezvous and docking systems for spacecraft. This display includes: photographs of the simulation hardware, plots of chase vehicle trajectories from simulations, pictures of the docking aid including image processing interpretations, and drawings of the control system strategy. Viewgraph-style sheets on the display bulletin board summarize the simulation objectives, benefits, special considerations, approach, and results.

Expedition 19 Docks to ISS

NASA Image and Video Library

2009-03-27

Mike Hawes, NASA's Acting Associate Administrator, left, looks on as Kirk Shireman, NASA's deputy ISS program manager, answers reporters questions during a Soyuz post-docking press conference at the Russian Mission Control Center in Korolev, Russia on Saturday March 28, 2009. The Soyuz TMA-14 docked to the International Space Station carrying Expedition 19 Commander Gennady I. Padalka, Flight Engineer Michael R. Barratt and Spaceflight Participant Charles Simonyi. Photo Credit: (NASA/Bill Ingalls)

FlexAID: Revisiting Docking on Non-Native-Complex Structures.

PubMed

Gaudreault, Francis; Najmanovich, Rafael J

2015-07-27

Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specific geometric criteria, based on surface complementarity. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. The prediction of binding poses is tested using the widely used Astex dataset as well as the HAP2 dataset, while performance in virtual screening is evaluated using a subset of the DUD dataset. We compare FlexAID to AutoDock Vina, FlexX, and rDock in an extensive number of scenarios to understand the strengths and limitations of the different programs as well as to reported results for Glide, GOLD, and DOCK6 where applicable. The most relevant among these scenarios is that of docking on flexible non-native-complex structures where as is the case in reality, the target conformation in the bound form is not known a priori. We demonstrate that FlexAID, unlike other programs, is robust against increasing structural variability. FlexAID obtains equivalent sampling success as GOLD and performs better than AutoDock Vina or FlexX in all scenarios against non-native-complex structures. FlexAID is better than rDock when there is at least one critical side-chain movement required upon ligand binding. In virtual screening, FlexAID results are lower on average than those of AutoDock Vina and rDock. The higher accuracy in flexible targets where critical movements are required, intuitive PyMOL-integrated graphical user interface and free source code as well as precompiled executables for Windows, Linux, and Mac OS make FlexAID a welcome addition to the arsenal of existing small-molecule protein docking methods.

The Rac-specific exchange factors Dock1 and Dock5 are dispensable for the establishment of the glomerular filtration barrier in vivo

PubMed Central

Laurin, Mélanie; Dumouchel, Annie; Fukui, Yoshinori; Côté, Jean-François

2013-01-01

Podocytes are specialized kidney cells that form the kidney filtration barrier through the connection of their foot processes. Nephrin and Neph family transmembrane molecules at the surface of podocytes interconnect to form a unique type of cell-cell junction, the slit diaphragm, which acts as a molecular sieve. The cytoplasmic tails of Nephrin and Neph mediate cytoskeletal rearrangement that contributes to the maintenance of the filtration barrier. Nephrin and Neph1 orthologs are essential to regulate cell-cell adhesion and Rac-dependent actin rearrangement during Drosophila myoblast fusion. We hypothesized here that molecules regulating myoblast fusion in Drosophila could contribute to signaling downstream of Nephrin and Neph1 in podocytes. We found that Nephrin engagement promoted recruitment of the Rac exchange factor Dock1 to the membrane. Furthermore, Nephrin overexpression led to lamellipodia formation that could be blocked by inhibiting Rac1 activity. We generated in vivo mouse models to investigate whether Dock1 and Dock5 contribute to the formation and maintenance of the kidney filtration barrier. Our results indicate that while Dock1 and Dock5 are expressed in podocytes, their functions are not essential for the development of the glomerular filtration barrier. Furthermore, mice lacking Dock1 were not protected from LPS-induced podocyte effacement. Our data suggest that Dock1 and Dock5 are not the important exchange factors regulating Rac activity during the establishment and maintenance of the glomerular barrier. PMID:24365888

last ATV docking OBT

NASA Image and Video Library

2014-08-07

ISS040-E-089629 (7 Aug. 2014) --- In the International Space Station?s Zvezda Service Module, European Space Agency astronaut Alexander Gerst (foreground) and Russian cosmonaut Alexander Skvortsov, both Expedition 40 flight engineers, participate in a training session in preparation for the rendezvous and docking of ESA?s fifth and final Automated Transfer Vehicle (ATV-5). Nicknamed the ?Georges Lemaitre? in honor of the Belgian physicist and astronomer who first proposed the Big Bang theory, ATV-5 will deliver more than seven tons of scientific experiments, food and other supplies when it docks to the aft end of Zvezda on Aug. 12.

last ATV docking OBT

NASA Image and Video Library

2014-08-07

ISS040-E-089627 (7 Aug. 2014) --- In the International Space Station?s Zvezda Service Module, European Space Agency astronaut Alexander Gerst (foreground) and Russian cosmonaut Alexander Skvortsov, both Expedition 40 flight engineers, participate in a training session in preparation for the rendezvous and docking of ESA?s fifth and final Automated Transfer Vehicle (ATV-5). Nicknamed the ?Georges Lemaitre? in honor of the Belgian physicist and astronomer who first proposed the Big Bang theory, ATV-5 will deliver more than seven tons of scientific experiments, food and other supplies when it docks to the aft end of Zvezda on Aug. 12.

Monte Carlo replica-exchange based ensemble docking of protein conformations.

PubMed

Zhang, Zhe; Ehmann, Uwe; Zacharias, Martin

2017-05-01

A replica-exchange Monte Carlo (REMC) ensemble docking approach has been developed that allows efficient exploration of protein-protein docking geometries. In addition to Monte Carlo steps in translation and orientation of binding partners, possible conformational changes upon binding are included based on Monte Carlo selection of protein conformations stored as ordered pregenerated conformational ensembles. The conformational ensembles of each binding partner protein were generated by three different approaches starting from the unbound partner protein structure with a range spanning a root mean square deviation of 1-2.5 Å with respect to the unbound structure. Because MC sampling is performed to select appropriate partner conformations on the fly the approach is not limited by the number of conformations in the ensemble compared to ensemble docking of each conformer pair in ensemble cross docking. Although only a fraction of generated conformers was in closer agreement with the bound structure the REMC ensemble docking approach achieved improved docking results compared to REMC docking with only the unbound partner structures or using docking energy minimization methods. The approach has significant potential for further improvement in combination with more realistic structural ensembles and better docking scoring functions. Proteins 2017; 85:924-937. © 2016 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

NASA Docking System (NDS) Interface Definitions Document (IDD)

NASA Technical Reports Server (NTRS)

Tabakman, Alexander; England, Warren

2013-01-01

The contents of this document define the integrated performance and interface design for NASA Docking System (NDS) Block 1 and the International Docking Adapter. The intent of this IDD is to provide the interface design for using, installing, and interfacing to the NDS Block 1 that will enable successful docking to the IDA. This document is under the control of the ISS Development Projects Office (OG).

Hydra Rendezvous and Docking Sensor

NASA Technical Reports Server (NTRS)

Roe, Fred; Carrington, Connie

2007-01-01

The U.S. technology to support a CEV AR&D activity is mature and was developed by NASA and supporting industry during an extensive research and development program conducted during the 1990's and early 2000 time frame at the Marshall Space Flight Center. Development and demonstration of a rendezvous/docking sensor was identified early in the AR&D Program as the critical enabling technology that allows automated proxinity operations and docking. A first generation rendezvous/docking sensor, the Video Guidance Sensor (VGS) was developed and successfully flown on STS 87 and again on STS 95, proving the concept of a video-based sensor. Advances in both video and signal processing technologies and the lessons learned from the two successful flight experiments provided a baseline for the development of a new generation of video based rendezvous/docking sensor. The Advanced Video Guidance Sensor (AVGS) has greatly increased performance and additional capability for longer-range operation. A Demonstration Automatic Rendezvous Technology (DART) flight experiment was flown in April 2005 using AVGS as the primary proximity operations sensor. Because of the absence of a docking mechanism on the target satellite, this mission did not demonstrate the ability of the sensor to coltrold ocking. Mission results indicate that the rendezvous sensor operated successfully in "spot mode" (2 km acquisition of the target, bearing data only) but was never commanded to "acquire and track" the docking target. Parts obsolescence issues prevent the construction of current design AVGS units to support the NASA Exploration initiative. This flight proven AR&D technology is being modularized and upgraded with additional capabilities through the Hydra project at the Marshall Space Flight Center. Hydra brings a unique engineering approach and sensor architecture to the table, to solve the continuing issues of parts obsolescence and multiple sensor integration. This paper presents an approach to

Orion Handling Qualities During ISS Proximity Operations and Docking

NASA Technical Reports Server (NTRS)

Stephens, John-Paul; Vos, Gordon A.; Bilimoria, Karl D.; Mueller, Eric R.; Brazzel, Jack; Spehar, Pete

2011-01-01

NASA's Orion spacecraft is designed to autonomously rendezvous and dock with many vehicles including the International Space Station. However, the crew is able to assume manual control of the vehicle s attitude and flight path. In these instances, Orion must meet handling qualities requirements established by NASA. Two handling qualities assessments were conducted at the Johnson Space Center to evaluate preliminary designs of the vehicle using a six degree of freedom, high-fidelity guidance, navigation, and control simulation. The first assessed Orion s handling qualities during the last 20 ft before docking, and included both steady and oscillatory motions of the docking target. The second focused on manual acquisition of the docking axis during the proximity operations phase and subsequent station-keeping. Cooper-Harper handling qualities ratings, workload ratings and comments were provided by 10 evaluation pilots for the docking study and 5 evaluation pilots for the proximity operations study. For the docking task, both cases received 90% Level 1 (satisfactory) handling qualities ratings, exceeding NASA s requirement. All ratings for the ProxOps task were Level 1. These evaluations indicate that Orion is on course to meet NASA's handling quality requirements for ProxOps and docking.

Tail docking in horses: a review of the issues.

PubMed

Lefebvre, D; Lips, D; Odberg, F O; Giffroy, J M

2007-09-01

Routinely performed painful procedures are of increasing interest and, in 2001 (Royal Order, May 17), Belgium prohibited docking in several vertebrates including horses. In 2004, opponents to this decision submitted a Bill (Doc51 0969/001) to Parliament, intending to obtain derogation for Belgian draught horses, which were traditionally docked. The Animal Welfare Council of Belgium, an official body advising the Minister of Public Health, was asked to evaluate this complex question, including biological, ethical and socio-economic aspects, on the basis of the available peer-reviewed studies. In this context, this study reviews legal aspects (overview of the European legislation), zootechnic aspects (uses of the Belgian draught horse) and biological aspects (pain potentially related to docking; horses' welfare linked to insect harassment and hygiene, communication and reproduction) of tail docking in draught horses. We conclude that (1) there is no benefit for horses in tail docking, including Belgian draught horses, (2) potential advantages of docking are essentially in favour of humans and these advantages could be scrupulously re-evaluated, taking into account practices of other countries. Therefore, there is no need to dock any horse other than for veterinary reasons.

Structure-based drug design: docking and scoring.

PubMed

Kroemer, Romano T

2007-08-01

This review gives an introduction into ligand - receptor docking and illustrates the basic underlying concepts. An overview of different approaches and algorithms is provided. Although the application of docking and scoring has led to some remarkable successes, there are still some major challenges ahead, which are outlined here as well. Approaches to address some of these challenges and the latest developments in the area are presented. Some aspects of the assessment of docking program performance are discussed. A number of successful applications of structure-based virtual screening are described.

13. ORE DOCK, LOOKING EAST FROM HULETT NO. 1. WHEN ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

13. ORE DOCK, LOOKING EAST FROM HULETT NO. 1. WHEN BUILT IN 1911-1912, THIS WAS THE LARGEST ORE-UNLOADING DOCK ON THE GREAT LAKES. THE DOCK FEATURED FOUR HULETT UNLOADERS, EACH WITH A BUCKET CAPACITY OF 17 TONS; A 15-TON CAPACITY ORE STOCKING AND REHANDLING BRIDGE; AND A ONE-MILLION-TON CAPACITY ORE STORAGE YARD. THE WILLIAM-SEAVER-MORGAN COMPANY OF CLEVELAND BUILT THE DOCK EQUIPMENT. - Pennsylvania Railway Ore Dock, Lake Erie at Whiskey Island, approximately 1.5 miles west of Public Square, Cleveland, Cuyahoga County, OH

Docking analysis of verteporfin with YAP WW domain.

PubMed

Kandoussi, Ilham; Lakhlili, Wiame; Taoufik, Jamal; Ibrahimi, Azeddine

2017-01-01

The YAP oncogene is a known cancer target. Therefore, it is of interest to understand the molecular docking interaction of verteporfin (a derivative of benzo-porphyrin) with the WW domain of YAP (clinically used for photo-dynamic therapy in macular degeneration) as a potential WW domain-ligand modulator by inhibition. A homology protein SWISS MODEL of the human YAP protein was constructed to dock (using AutoDock vina) with the PubChem verteporfin structure for interaction analysis. The docking result shows the possibilities of verteporfin interaction with the oncogenic transcription cofactor YAP having WW1 and WW2 domains. Thus, the ability of verteporfin to bind with the YAP WW domain having modulator activity is implied in this analysis.

SpaceDock: A Performance Task Platform for Spaceflight Operations

NASA Technical Reports Server (NTRS)

Marshburn, Thomas H.; Strangman, Gary E.; Strauss, Monica S.; Sutton, Jeffrey P.

2003-01-01

Preliminary evidence during both short- and long-duration spaceflight indicates that perceptual-motor coordination changes occur and persist in-flight. However, there is presently no in-flight method for evaluating astronaut performance on mission-critical tasks such as docking. We present a portable platform we have developed for attempting and evaluating docking, and describe the results of a pilot study wherein flight novices learned the docking task. Methods: A dual-joystick, six degrees of freedom platform-called SpaceDock-was developed to enable portable, adaptable performance testing in a spaceflight operations setting. Upon this platform, a simplified docking task was created, involving a constant rate of approach towards a docking target and requiring the user to correct translation in two dimensions and attitude orientation along one dimension (either pitch or roll). Ten flight naive subjects performed the task over a 45 min period and all joystick inputs and timings were collected, from which we could successfully reconstruct travel paths, input profiles and relative target displacements. Results: Subjects exhibited significant improvements in docking over the course of the experiment. Learning to compensate for roll-alterations was robust, whereas compensation for pitch-alterations was not in evidence in this population and relatively short training period. Conclusion: The SpaceDock platform can provide a novel method for training and testing subjects, on a spaceflight-relevant task, and can be used to examine behavioral learning, strategy use, and has been adapted for use in brain imaging experiments.

New docking target taped to middeck locker

NASA Image and Video Library

1996-09-20

STS79-E-5104 (20 September 1996) --- The STS-79 crew members removed the docking target from the Docking Module (DM) and attached it to a locker door to photograph it and examine a slight peel on the surface, during Flight Day 5.

75 FR 78601 - Drawbridge Operation Regulation; Gulf Intracoastal Waterway, New Orleans Harbor, Inner Harbor...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-16

... Operation Regulation; Gulf Intracoastal Waterway, New Orleans Harbor, Inner Harbor Navigation Canal, New Orleans, Orleans Parish, LA AGENCY: Coast Guard, DHS. ACTION: Notice of temporary deviation from... Harvey Lock), at New Orleans, Orleans Parish, Louisiana. This deviation is necessary to adjust the...

FPGA acceleration of rigid-molecule docking codes

PubMed Central

Sukhwani, B.; Herbordt, M.C.

2011-01-01

Modelling the interactions of biological molecules, or docking, is critical both to understanding basic life processes and to designing new drugs. The field programmable gate array (FPGA) based acceleration of a recently developed, complex, production docking code is described. The authors found that it is necessary to extend their previous three-dimensional (3D) correlation structure in several ways, most significantly to support simultaneous computation of several correlation functions. The result for small-molecule docking is a 100-fold speed-up of a section of the code that represents over 95% of the original run-time. An additional 2% is accelerated through a previously described method, yielding a total acceleration of 36× over a single core and 10× over a quad-core. This approach is found to be an ideal complement to graphics processing unit (GPU) based docking, which excels in the protein–protein domain. PMID:21857870

istar: a web platform for large-scale protein-ligand docking.

PubMed

Li, Hongjian; Leung, Kwong-Sak; Ballester, Pedro J; Wong, Man-Hon

2014-01-01

Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. istar

Protein-protein docking using region-based 3D Zernike descriptors

PubMed Central

2009-01-01

Background Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. Results We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-αRMSD ≤ 2.5 Å) within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. Conclusion We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction

Protein-protein docking using region-based 3D Zernike descriptors.

PubMed

Venkatraman, Vishwesh; Yang, Yifeng D; Sael, Lee; Kihara, Daisuke

2009-12-09

Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-alphaRMSD < or = 2.5 A) within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction. Rigorous benchmark studies

Experimental validation of docking and capture using space robotics testbeds

NASA Technical Reports Server (NTRS)

Spofford, John

1991-01-01

Docking concepts include capture, berthing, and docking. The definitions of these terms, consistent with AIAA, are as follows: (1) capture (grasping)--the use of a manipulator to make initial contact and attachment between transfer vehicle and a platform; (2) berthing--positioning of a transfer vehicle or payload into platform restraints using a manipulator; and (3) docking--propulsive mechanical connection between vehicle and platform. The combination of the capture and berthing operations is effectively the same as docking; i.e., capture (grasping) + berthing = docking. These concepts are discussed in terms of Martin Marietta's ability to develop validation methods using robotics testbeds.

Overview of LIDS Docking Seals Development

NASA Technical Reports Server (NTRS)

Dunlap, Pat; Steinetz, Bruce; Daniels, Chris

2008-01-01

NASA is developing a new docking system to support future space exploration missions to low-Earth orbit, the Moon, and Mars. This mechanism, called the Low Impact Docking System (LIDS), is designed to connect pressurized space vehicles and structures including the Crew Exploration Vehicle, International Space Station, and lunar lander. NASA Glenn Research Center (GRC) is playing a key role in developing the main interface seal for this new docking system. These seals will be approximately 147 cm (58 in.) in diameter. GRC is evaluating the performance of candidate seal designs under simulated operating conditions at both sub-scale and full-scale levels. GRC is ultimately responsible for delivering flight hardware seals to NASA Johnson Space Center around 2013 for integration into LIDS flight units.

Expedition 55 Soyuz Docking

NASA Image and Video Library

2018-03-23

Icons for the International Space Station and Soyuz MS-08 spacecraft are seen on a tracking map on a screen in the Moscow Mission Control Center as the spacecraft approaches for docking, Friday, March 23, 2018 in Korolev, Russia. The Soyuz MS-08 spacecraft carrying Expedition 55-56 crewmembers Oleg Artemyev of Roscosmos and Ricky Arnold and Drew Feustel of NASA docked at 3:40 p.m. Eastern time (10:40 p.m. Moscow time) on March 23 and joined Expedition 55 Commander Anton Shkaplerov of Roscosmos, Scott Tingle of NASA, and Norishige Kanai of the Japan Aerospace Exploration Agency (JAXA). Photo Credit: (NASA/Joel Kowsky)

Expedition 55 Soyuz Docking

NASA Image and Video Library

2018-03-23

Guests watch a live view of the International Space Station, as seen by cameras onboard the Soyuz MS-08 spacecraft with Expedition 55-56 crewmembers Oleg Artemyev of Roscosmos and Ricky Arnold and Drew Feustel of NASA, on screens at the Moscow Mission Control Center as the spacecraft approaches for docking, Friday, March 23, 2018 in Korolev, Russia. The Soyuz MS-08 spacecraft carrying Artemyev, Feustel, and Arnold docked at 3:40 p.m. Eastern time (10:40 p.m. Moscow time) and joined Expedition 55 Commander Anton Shkaplerov of Roscosmos, Scott Tingle of NASA, and Norishige Kanai of the Japan Aerospace Exploration Agency (JAXA). Photo Credit: (NASA/Joel Kowsky)

Expedition 55 Soyuz Docking

NASA Image and Video Library

2018-03-23

A live view of the International Space Station, as seen by cameras onboard the Soyuz MS-08 spacecraft with Expedition 55-56 crewmembers Oleg Artemyev of Roscosmos and Ricky Arnold and Drew Feustel of NASA, is seen on screens at the Moscow Mission Control Center as the spacecraft approaches for docking, Friday, March 23, 2018 in Korolev, Russia. The Soyuz MS-08 spacecraft carrying Artemyev, Feustel, and Arnold docked at 3:40 p.m. Eastern time (10:40 p.m. Moscow time) and joined Expedition 55 Commander Anton Shkaplerov of Roscosmos, Scott Tingle of NASA, and Norishige Kanai of the Japan Aerospace Exploration Agency (JAXA). Photo Credit: (NASA/Joel Kowsky)

Expedition 54 Soyuz Docking

NASA Image and Video Library

2017-12-19

Icons for the International Space Station and Soyuz MS-07 spacecraft are seen on a tracking map on a screen in the Moscow Mission Control Center as the spacecraft approaches for docking, Tuesday, Dec. 19, 2017 in Korolev, Russia. The Soyuz MS-07 spacecraft carrying Anton Shkaplerov of Roscosmos, Scott Tingle of NASA, and Norishige Kanai of the Japan Aerospace Exploration Agency (JAXA) docked with the International Space Station at 3:39 a.m. EST, Tuesday, Dec. 19 while 250 statute miles over the southern coast of Italy and joined Expedition 54 Commander Alexander Misurkin of Roscosmos, and NASA astronauts Joe Acaba and Mark Vande Hei. Photo Credit: (NASA/Joel Kowsky)

33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

Code of Federal Regulations, 2012 CFR

2012-07-01

... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone... entrance of the harbor connecting coordinates 41°51′09″ N, 087°36′36″W and 41°51′11″ N, 087°36′22″ W. (b...

33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

Code of Federal Regulations, 2014 CFR

2014-07-01

... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone... entrance of the harbor connecting coordinates 41°51′09″ N, 087°36′36″ W and 41°51′11″ N, 087°36′22″ W. (b...

33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

Code of Federal Regulations, 2013 CFR

2013-07-01

... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone... entrance of the harbor connecting coordinates 41°51′09″ N, 087°36′36″W and 41°51′11″ N, 087°36′22″ W. (b...

Docking analysis of verteporfin with YAP WW domain

PubMed Central

Kandoussi, Ilham; Lakhlili, Wiame; Taoufik, Jamal; Ibrahimi, Azeddine

2017-01-01

The YAP oncogene is a known cancer target. Therefore, it is of interest to understand the molecular docking interaction of verteporfin (a derivative of benzo-porphyrin) with the WW domain of YAP (clinically used for photo-dynamic therapy in macular degeneration) as a potential WW domain-ligand modulator by inhibition. A homology protein SWISS MODEL of the human YAP protein was constructed to dock (using AutoDock vina) with the PubChem verteporfin structure for interaction analysis. The docking result shows the possibilities of verteporfin interaction with the oncogenic transcription cofactor YAP having WW1 and WW2 domains. Thus, the ability of verteporfin to bind with the YAP WW domain having modulator activity is implied in this analysis. PMID:28943729

Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2

NASA Astrophysics Data System (ADS)

Kadukova, Maria; Grudinin, Sergei

2018-01-01

The 2016 D3R Grand Challenge 2 provided an opportunity to test multiple protein-ligand docking protocols on a set of ligands bound to farnesoid X receptor that has many available experimental structures. We participated in the Stage 1 of the Challenge devoted to the docking pose predictions, with the mean RMSD value of our submission poses of 2.9 Å. Here we present a thorough analysis of our docking predictions made with AutoDock Vina and the Convex-PL rescoring potential by reproducing our submission protocol and running a series of additional molecular docking experiments. We conclude that a correct receptor structure, or more precisely, the structure of the binding pocket, plays the crucial role in the success of our docking studies. We have also noticed the important role of a local ligand geometry, which seems to be not well discussed in literature. We succeed to improve our results up to the mean RMSD value of 2.15-2.33 Å dependent on the models of the ligands, if docking these to all available homologous receptors. Overall, for docking of ligands of diverse chemical series we suggest to perform docking of each of the ligands to a set of multiple receptors that are homologous to the target.

Linear Actuator System for the NASA Docking System

NASA Technical Reports Server (NTRS)

Dick, Brandon N.; Oesch, Christopher; Rupp, Timothy W.

2017-01-01

The Linear Actuator System (LAS) is a major sub-system within the NASA Docking System (NDS). The NDS Block 1 will be used on the Boeing Crew Space Transportation (CST-100) system to achieve docking with the International Space Station. Critical functions in the Soft Capture aspect of docking are performed by the LAS. This paper describes the general function of the LAS, the system's key requirements and technical challenges, and the development and qualification approach for the system.

Influence of the Pearl River estuary and vertical mixing in Victoria Harbor on water quality in relation to eutrophication impacts in Hong Kong waters.

PubMed

Yin, Kedong; Harrison, Paul J

2007-06-01

This study presents water quality parameters such as nutrients, phytoplankton biomass and dissolved oxygen based on 11 years of water quality data in Victoria Harbor and examined how the Pearl River estuary discharge in summer and year round sewage discharge influenced these parameters. Nutrients in Victoria Harbor were strongly influenced by both the Pearl River and sewage effluent, as indicated by the high NO(3) inputs from the Pearl River in summer and higher NH(4) and PO(4) in Victoria Harbor than both its sides. N:P ratios were low in the dry season, but increased to >16:1 in the wet season, suggesting that P is potentially the most limiting nutrient in this area during the critical period in the summer. Although there were generally high nutrients, the phytoplankton biomass was not as high as one would expect in Victoria Harbor. In fact, there were high concentrations of chl near the bottom well below the photic zone. Salinity near the bottom was lower in Victoria Harbor than at the two entrances to Victoria Harbor, suggesting strong vertical mixing within Victoria Harbor. Therefore, strong vertical mixing and horizontal advection appear to play an important role in significantly reducing eutrophication impacts in Victoria Harbor. Consequently, dissolved oxygen near the bottom was low in summer, but only occasionally dipped to 2 mgL(-1) despite the high organic loading from sewage effluent.

Technology Development of Automated Rendezvous and Docking/Capture Sensors and Docking Mechanism for the Asteroid Redirect Crewed Mission

NASA Technical Reports Server (NTRS)

Hinkel, Heather; Cryan, Scott; Zipay, John; Strube, Matthew

2015-01-01

This paper will describe the technology development efforts NASA has underway for Automated Rendezvous and Docking/Capture (AR&D/C) sensors and a docking mechanism and the challenges involved. The paper will additionally address how these technologies will be extended to other missions requiring AR&D/C whether robotic or manned. NASA needs AR&D/C sensors for both the robotic and crewed segments of the Asteroid Redirect Mission (ARM). NASA recently conducted a commonality assessment of the concept of operations for the robotic Asteroid Redirect Vehicle (ARV) and the crewed mission segment using the Orion crew vehicle. The commonality assessment also considered several future exploration and science missions requiring an AR&D/C capability. Missions considered were asteroid sample return, satellite servicing, and planetary entry, descent, and landing. This assessment determined that a common sensor suite consisting of one or more visible wavelength cameras, a threedimensional LIDAR along with long-wavelength infrared cameras for robustness and situational awareness could be used on each mission to eliminate the cost of multiple sensor developments and qualifications. By choosing sensor parameters at build time instead of at design time and, without having to requalify flight hardware, a specific mission can design overlapping bearing, range, relative attitude, and position measurement availability to suit their mission requirements with minimal nonrecurring engineering costs. The resulting common sensor specification provides the union of all performance requirements for each mission and represents an improvement over the current systems used for AR&D/C today. These sensor specifications are tightly coupled to the docking system capabilities and requirements for final docking conditions. The paper will describe NASA's efforts to develop a standard docking system for use across NASA human spaceflight missions to multiple destinations. It will describe the current

Technology Development of Automated Rendezvous and Docking/Capture Sensors and Docking Mechanism for the Asteroid Redirect Crewed Mission

NASA Technical Reports Server (NTRS)

Hinkel, Heather; Strube, Matthew; Zipay, John J.; Cryan, Scott

2015-01-01

This paper will describe the technology development efforts NASA has underway for Automated Rendezvous and Docking/Capture (AR and D/C) sensors and a docking mechanism and the challenges involved. The paper will additionally address how these technologies will be extended to other missions requiring AR and D/C whether robotic or manned. NASA needs AR&D/C sensors for both the robotic and crewed segments of the Asteroid Redirect Mission (ARM). NASA recently conducted a commonality assessment of the concept of operations for the robotic Asteroid Redirect Vehicle (ARV) and the crewed mission segment using the Orion crew vehicle. The commonality assessment also considered several future exploration and science missions requiring an AR and D/C capability. Missions considered were asteroid sample return, satellite servicing, and planetary entry, descent, and landing. This assessment determined that a common sensor suite consisting of one or more visible wavelength cameras, a threedimensional LIDAR along with long-wavelength infrared cameras for robustness and situational awareness could be used on each mission to eliminate the cost of multiple sensor developments and qualifications. By choosing sensor parameters at build time instead of at design time and, without having to requalify flight hardware, a specific mission can design overlapping bearing, range, relative attitude, and position measurement availability to suit their mission requirements with minimal nonrecurring engineering costs. The resulting common sensor specification provides the union of all performance requirements for each mission and represents an improvement over the current systems used for AR and D/C today. These sensor specifications are tightly coupled to the docking system capabilities and requirements for final docking conditions. The paper will describe NASA's efforts to develop a standard docking system for use across NASA human spaceflight missions to multiple destinations. It will describe

Technology Development of Automated Rendezvous and Docking/Capture Sensors and Docking Mechanism for the Asteroid Redirect Crewed Mission

NASA Technical Reports Server (NTRS)

Hinkel, Heather; Strube, Matthew; Zipay, John J.; Cryan, Scott

2016-01-01

This paper will describe the technology development efforts NASA has underway for Automated Rendezvous and Docking/Capture (AR&D/C) sensors and a docking mechanism and the challenges involved. The paper will additionally address how these technologies will be extended to other missions requiring AR&D/C whether robotic or manned. NASA needs AR&D/C sensors for both the robotic and crewed segments of the Asteroid Redirect Mission (ARM). NASA recently conducted a commonality assessment of the concept of operations for the robotic Asteroid Redirect Vehicle (ARV) and the crewed mission segment using the Orion spacecraft. The commonality assessment also considered several future exploration and science missions requiring an AR&D/C capability. Missions considered were asteroid sample return, satellite servicing, and planetary entry, descent, and landing. This assessment determined that a common sensor suite consisting of one or more visible wavelength cameras, a three-dimensional LIDAR along with long-wavelength infrared cameras for robustness and situational awareness could be used on each mission to eliminate the cost of multiple sensor developments and qualifications. By choosing sensor parameters at build-time instead of at design-time and, without having to requalify flight hardware, a specific mission can design overlapping bearing, range, relative attitude, and position measurement availability to suit their mission requirements with minimal non-recurring engineering costs. The resulting common sensor specification provides the union of all performance requirements for each mission and represents an improvement over the current systems used for AR&D/C today. These sensor specifications are tightly coupled to the docking system capabilities and requirements for final docking conditions. The paper will describe NASA's efforts to develop a standard docking system for use across NASA human spaceflight missions to multiple destinations. It will describe the current

Expedition 28 Docking

NASA Image and Video Library

2011-06-10

Guests at the Russian Mission Control Center in Korolove, Russia watch on a large screen TV as the Soyuz TMA-02M nears its docking to the International Space Station on Friday, June 10, 2011. Photo Credit: (NASA/Carla Cioffi)

ARCADE small-scale docking mechanism for micro-satellites

NASA Astrophysics Data System (ADS)

Boesso, A.; Francesconi, A.

2013-05-01

The development of on-orbit autonomous rendezvous and docking (ARD) capabilities represents a key point for a number of appealing mission scenarios that include activities of on-orbit servicing, automated assembly of modular structures and active debris removal. As of today, especially in the field of micro-satellites ARD, many fundamental technologies are still missing or require further developments and micro-gravity testing. In this framework, the University of Padova, Centre of Studies and Activities for Space (CISAS), developed the Autonomous Rendezvous Control and Docking Experiment (ARCADE), a technology demonstrator intended to fly aboard a BEXUS stratospheric balloon. The goal was to design, build and test, in critical environment conditions, a proximity relative navigation system, a custom-made reaction wheel and a small-size docking mechanism. The ARCADE docking mechanism was designed against a comprehensive set of requirements and it can be classified as small-scale, central, gender mating and unpressurized. The large use of commercial components makes it low-cost and simple to be manufactured. Last, it features a good tolerance to off-nominal docking conditions and a by-design soft docking capability. The final design was extensively verified to be compliant with its requirements by means of numerical simulations and physical testing. In detail, the dynamic behaviour of the mechanism in both nominal and off-nominal conditions was assessed with the multibody dynamics analysis software MD ADAMS 2010 and functional tests were carried out within the fully integrated ARCADE experiment to ensure the docking system efficacy and to highlight possible issues. The most relevant results of the study will be presented and discussed in conclusion to this paper.

Improving Docking Performance Using Negative Image-Based Rescoring.

PubMed

Kurkinen, Sami T; Niinivehmas, Sanna; Ahinko, Mira; Lätti, Sakari; Pentikäinen, Olli T; Postila, Pekka A

2018-01-01

Despite the large computational costs of molecular docking, the default scoring functions are often unable to recognize the active hits from the inactive molecules in large-scale virtual screening experiments. Thus, even though a correct binding pose might be sampled during the docking, the active compound or its biologically relevant pose is not necessarily given high enough score to arouse the attention. Various rescoring and post-processing approaches have emerged for improving the docking performance. Here, it is shown that the very early enrichment (number of actives scored higher than 1% of the highest ranked decoys) can be improved on average 2.5-fold or even 8.7-fold by comparing the docking-based ligand conformers directly against the target protein's cavity shape and electrostatics. The similarity comparison of the conformers is performed without geometry optimization against the negative image of the target protein's ligand-binding cavity using the negative image-based (NIB) screening protocol. The viability of the NIB rescoring or the R-NiB, pioneered in this study, was tested with 11 target proteins using benchmark libraries. By focusing on the shape/electrostatics complementarity of the ligand-receptor association, the R-NiB is able to improve the early enrichment of docking essentially without adding to the computing cost. By implementing consensus scoring, in which the R-NiB and the original docking scoring are weighted for optimal outcome, the early enrichment is improved to a level that facilitates effective drug discovery. Moreover, the use of equal weight from the original docking scoring and the R-NiB scoring improves the yield in most cases.

Pearl Harbor Biological Survey

DTIC Science & Technology

1974-08-30

properties, uses, and driving mechanisms affecting the harbor is given. The methods of obtaining current data, salinity profiles, and temperature... salinities were used for each calibration In order to check the salinity computation mechanism of the Instrument. Temperature calibrations were...Water Temperature Contours for Navy Thermal Discharges 3.2-23 3.2-7. General Layout of Pearl Harbor Showing Mean Monthly Salinity (3L) Variation

A modular docking mechanism for in-orbit assembly and spacecraft servicing

NASA Technical Reports Server (NTRS)

Gampe, F.; Priesett, K.; Bentall, R. H.

1985-01-01

A Docking Mechanism concept is described which is suitable for use with autonomous docking systems. The central feature of using simple cylindrical handles on one side and a type of prism seating on the other is offered as a practical method of achieving a standardized structural interface without freezing continued development of the latches, either technically or commercially. The main emphasis in docking mechanism concepts is in two directions: (1) a very simple docking mechanism, involving mainly the latch mechanism to achieve a structural link; and (2) a sophisticated Docking Mechanism, where the latch mechanism is designed for nonrigid spacecraft and the achievement of very low dynamic interactions between spacecraft during the docking process.

A web interface for easy flexible protein-protein docking with ATTRACT.

PubMed

de Vries, Sjoerd J; Schindler, Christina E M; Chauvot de Beauchêne, Isaure; Zacharias, Martin

2015-02-03

Protein-protein docking programs can give valuable insights into the structure of protein complexes in the absence of an experimental complex structure. Web interfaces can facilitate the use of docking programs by structural biologists. Here, we present an easy web interface for protein-protein docking with the ATTRACT program. While aimed at nonexpert users, the web interface still covers a considerable range of docking applications. The web interface supports systematic rigid-body protein docking with the ATTRACT coarse-grained force field, as well as various kinds of protein flexibility. The execution of a docking protocol takes up to a few hours on a standard desktop computer. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Analyses of the dynamic docking test system for advanced mission docking system test programs. [Apollo Soyuz Test Project

NASA Technical Reports Server (NTRS)

Gates, R. M.; Williams, J. E.

1974-01-01

Results are given of analytical studies performed in support of the design, implementation, checkout and use of NASA's dynamic docking test system (DDTS). Included are analyses of simulator components, a list of detailed operational test procedures, a summary of simulator performance, and an analysis and comparison of docking dynamics and loads obtained by test and analysis.

Sediment toxicity in Savannah Harbor

USGS Publications Warehouse

Winger, P.V.; Lasier, P.J.

1995-01-01

Savannah Harbor, located near the mouth of the Savannah River, Georgia and South Carolina, is impacted by industrial and municipal effluents. Potential release of contaminants stored in harbor sediments through dredging and shipping operations requires that contaminated areas be identified for proper management of the system and protection of wildlife resources. During 1991, Hyalella azteca were exposed in 10-d static-renewal toxicity tests to pore-water and solid-phase sediment samples collected from 26 sites within Savannah Harbor. Pore-water toxicity was more pronounced than that for solidphase sediment. Toxicity and reduced leaf consumption demonstrated impaired sediment quality at specific sites within Savannah Harbor and Back River. Factors responsible for the decreased sediment quality were ammonia, alkalinity, and metal concentrations (cadmium, chromium, lead, molybdenum, and nickel). Elevated concentrations of metals and toxicities in Back River sediments indicated impacts from adjacent dredge-spoil areas.

33 CFR 80.1122 - Channel Islands Harbor, CA.

Code of Federal Regulations, 2012 CFR

2012-07-01

... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Channel Islands Harbor, CA. 80...

33 CFR 80.1122 - Channel Islands Harbor, CA.

Code of Federal Regulations, 2010 CFR

2010-07-01

... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Channel Islands Harbor, CA. 80...

33 CFR 80.1122 - Channel Islands Harbor, CA.

Code of Federal Regulations, 2014 CFR

2014-07-01

... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Channel Islands Harbor, CA. 80...

33 CFR 80.1122 - Channel Islands Harbor, CA.

Code of Federal Regulations, 2013 CFR

2013-07-01

... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Channel Islands Harbor, CA. 80...

33 CFR 80.1122 - Channel Islands Harbor, CA.

Code of Federal Regulations, 2011 CFR

2011-07-01

... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Channel Islands Harbor, CA. 80...

17. ORE DOCK, LOOKING EAST FROM HULETT NO. 1. WHEN ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

17. ORE DOCK, LOOKING EAST FROM HULETT NO. 1. WHEN BUILT IN 1911-1912, THIS WAS THE LARGEST ORE-UNLOADING DOCK ON THE GREAT LAKES. - Pennsylvania Railway Ore Dock, Lake Erie at Whiskey Island, approximately 1.5 miles west of Public Square, Cleveland, Cuyahoga County, OH

Recent progress and future directions in protein-protein docking.

PubMed

Ritchie, David W

2008-02-01

This article gives an overview of recent progress in protein-protein docking and it identifies several directions for future research. Recent results from the CAPRI blind docking experiments show that docking algorithms are steadily improving in both reliability and accuracy. Current docking algorithms employ a range of efficient search and scoring strategies, including e.g. fast Fourier transform correlations, geometric hashing, and Monte Carlo techniques. These approaches can often produce a relatively small list of up to a few thousand orientations, amongst which a near-native binding mode is often observed. However, despite the use of improved scoring functions which typically include models of desolvation, hydrophobicity, and electrostatics, current algorithms still have difficulty in identifying the correct solution from the list of false positives, or decoys. Nonetheless, significant progress is being made through better use of bioinformatics, biochemical, and biophysical information such as e.g. sequence conservation analysis, protein interaction databases, alanine scanning, and NMR residual dipolar coupling restraints to help identify key binding residues. Promising new approaches to incorporate models of protein flexibility during docking are being developed, including the use of molecular dynamics snapshots, rotameric and off-rotamer searches, internal coordinate mechanics, and principal component analysis based techniques. Some investigators now use explicit solvent models in their docking protocols. Many of these approaches can be computationally intensive, although new silicon chip technologies such as programmable graphics processor units are beginning to offer competitive alternatives to conventional high performance computer systems. As cryo-EM techniques improve apace, docking NMR and X-ray protein structures into low resolution EM density maps is helping to bridge the resolution gap between these complementary techniques. The use of symmetry and

STS-74 view of MIR Docking module at Pad 39A

NASA Technical Reports Server (NTRS)

1995-01-01

Workers at Launch Pad 39A are preparing to close the payload bay doors on the Space Shuttle Atlantis for its upcoming launch on Mission STS-74 and the second docking with the Russian Space Station Mir. Uppermost in the payload bay is the Orbiter Docking System (ODS), which also flew on the first docking flight between the Space Shuttle and MIR. Lowermost is the primary payload of STS-74, the Russian-built Docking Module. During the mission, the Docking Module will first be attached to ODS and then to Mir. It will be left attached to Mir to become a permanent extension that will afford adequate clearance between the orbiter and the station during future dockings. At left in the payload bay, looking like a very long pole, is the Canadian-built Remote Manipulator System arm that will be used by the crew to hoist the Docking Module and attach it to the ODS.

The Boston Harbor Project, and large decreases in loadings of eutrophication-related materials to Boston Harbor.

PubMed

Taylor, David I

2010-04-01

Boston Harbor, a bay-estuary in the north-east USA, has recently been the site of one of the largest wastewater infrastructure projects conducted in the USA, the Boston Harbor Project (BHP). The BHP, which was conducted from 1991 to 2000, ended over a century of direct wastewater treatment facility discharges to the harbor. The BHP caused the loadings of total nitrogen (TN), total phosphorus (TP), total suspended solids (TSS) and particulate organic carbon (POC) to the harbor, to decrease by between 80% and 90%. Approximately one-third of the decreases in TSS and POC loadings occurred between 1991 and 1992; the remaining two-thirds, between 1995 and 2000. For TN and TP, the bulk of the decreases occurred between 1997 or 1998, and 2000. (c) 2009 Elsevier Ltd. All rights reserved.

Game Theoretic Approach to Post-Docked Satellite Control

NASA Technical Reports Server (NTRS)

Hiramatsu, Takashi; Fitz-Coy, Norman G.

2007-01-01

This paper studies the interaction between two satellites after docking. In order to maintain the docked state with uncertainty in the motion of the target vehicle, a game theoretic controller with Stackelberg strategy to minimize the interaction between the satellites is considered. The small perturbation approximation leads to LQ differential game scheme, which is validated to address the docking interactions between a service vehicle and a target vehicle. The open-loop solution are compared with Nash strategy, and it is shown that less control efforts are obtained with Stackelberg strategy.

A multipurpose model of Hermes-Columbus docking mechanism

NASA Technical Reports Server (NTRS)

Gonzalez-Vallejo, J. J.; Fehse, W.; Tobias, A.

1992-01-01

One of the foreseen missions of the HERMES spacevehicle is the servicing to the Columbus Free Flying Laboratory (MTFF). Docking between the two spacecraft is a critical operation in which the Docking Mechanism (DM) has a major role. In order to analyze and assess robustness of initially selected concepts and to identify suitable implementation solutions, through the investigation of main parameters involved in the docking functions, a multipurpose model of DM was developed and tested. This paper describes the main design features as well as the process of calibrating and testing.

Linear Actuator System for the NASA Docking System

NASA Technical Reports Server (NTRS)

Dick, Brandon; Oesch, Chris

2017-01-01

The Linear Actuator System (LAS) is a major sub-system within the NASA Docking System (NDS). The NDS Block 1 will be used on the Boeing Crew Space Transportation (CST-100) system to achieve docking with the International Space Station. Critical functions in the Soft Capture aspect of docking are performed by the LAS, which implements the Soft Impact Mating and Attenuation Concept (SIMAC). This paper describes the general function of the LAS, the system's key requirements and technical challenges, and the development and qualification approach for the system.

33 CFR 110.38 - Edgartown Harbor, Mass.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner harbor...

33 CFR 110.38 - Edgartown Harbor, Mass.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner harbor...

33 CFR 110.38 - Edgartown Harbor, Mass.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner harbor...

33 CFR 110.38 - Edgartown Harbor, Mass.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner harbor...

33 CFR 110.38 - Edgartown Harbor, Mass.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner harbor...

Tail Docking of Canine Puppies: Reassessment of the Tail's Role in Communication, the Acute Pain Caused by Docking and Interpretation of Behavioural Responses.

PubMed

Mellor, David J

2018-05-31

Laws, regulations and professional standards increasingly aim to ban or restrict non-therapeutic tail docking in canine puppies. These constraints have usually been justified by reference to loss of tail participation in communication between dogs, the acute pain presumed to be caused during docking itself, subsequent experiences of chronic pain and heightened pain sensitivity, and the occurrence of other complications. These areas are reconsidered here. First, a scientifically robust examination of the dynamic functional foundations, sensory components and key features of body language that are integral to canine communication shows that the role of the tail has been greatly underestimated. More specifically, it shows that tail behaviour is so embedded in canine communication that docking can markedly impede unambiguous interactions between different dogs and between dogs and people. These interactions include the expression of wide ranges of both negative and positive emotions, moods and intentions that are of daily significance for dog welfare. Moreover, all docked dogs may experience these impediments throughout their lives, which challenges assertions by opponents to such bans or restrictions that the tail is a dispensable appendage. Second, and in contrast, a re-examination of the sensory capacities of canine puppies reveals that they cannot consciously experience acute or chronic pain during at least the first week after birth, which is when they are usually docked. The contrary view is based on questionable between-species extrapolation of information about pain from neurologically mature newborns such as calves, lambs, piglets and human infants, which certainly can consciously experience pain in response to injury, to neurologically immature puppies which remain unconscious and therefore unable to experience pain until about two weeks after birth. Third, underpinned by the incorrect conclusion that puppies are conscious at the usual docking age, it is

ConsDock: A new program for the consensus analysis of protein-ligand interactions.

PubMed

Paul, Nicodème; Rognan, Didier

2002-06-01

Protein-based virtual screening of chemical libraries is a powerful technique for identifying new molecules that may interact with a macromolecular target of interest. Because of docking and scoring limitations, it is more difficult to apply as a lead optimization method because it requires that the docking/scoring tool is able to propose as few solutions as possible and all of them with a very good accuracy for both the protein-bound orientation and the conformation of the ligand. In the present study, we present a consensus docking approach (ConsDock) that takes advantage of three widely used docking tools (Dock, FlexX, and Gold). The consensus analysis of all possible poses generated by several docking tools is performed sequentially in four steps: (i) hierarchical clustering of all poses generated by a docking tool into families represented by a leader; (ii) definition of all consensus pairs from leaders generated by different docking programs; (iii) clustering of consensus pairs into classes, represented by a mean structure; and (iv) ranking the different means starting from the most populated class of consensus pairs. When applied to a test set of 100 protein-ligand complexes from the Protein Data Bank, ConsDock significantly outperforms single docking with respect to the docking accuracy of the top-ranked pose. In 60% of the cases investigated here, ConsDock was able to rank as top solution a pose within 2 A RMSD of the X-ray structure. It can be applied as a postprocessing filter to either single- or multiple-docking programs to prioritize three-dimensional guided lead optimization from the most likely docking solution. Copyright 2002 Wiley-Liss, Inc.

Docking Mechanism on Progress 52

NASA Image and Video Library

2014-02-03

ISS038-E-041175 (3 Feb. 2014) --- This close-up view shows the docking mechanism of the unpiloted Russian ISS Progress 52 resupply ship as it undocks from the International Space Station's Pirs Docking Compartment at 11:21 a.m. (EST) on Feb. 3, 2014. The Progress backed away to a safe distance from the orbital complex to begin several days of tests to study thermal effects of space on its attitude control system. Filled with trash and other unneeded items, the Russian resupply ship will be commanded to re-enter Earth's atmosphere Feb. 11 and disintegrate harmlessly over the Pacific Ocean.

21. ORE DOCK, LOOKING SOUTHWEST. THIS VIEW SHOWS THE WEST ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

21. ORE DOCK, LOOKING SOUTHWEST. THIS VIEW SHOWS THE WEST END OF THE DOCK. EMPTY CARS ARE MOVED IN FROM THE WEST BY 'SHUNT CARS,' PUT INTO PLACE AS NEEDED BENEATH THE HULETTS, FILLED, THEN SHUNTED TO THE EAST END OF THE YARD WHERE THEY ARE MADE UP INTO TRAINS. THE POWER HOUSE (WITH TALL ARCHED WINDOWS) AND THE TWO-STORY DOCK OFFICE CAN BE SEEN HERE. - Pennsylvania Railway Ore Dock, Lake Erie at Whiskey Island, approximately 1.5 miles west of Public Square, Cleveland, Cuyahoga County, OH

The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators

NASA Astrophysics Data System (ADS)

Taha, Mutasem O.; Habash, Maha; Khanfar, Mohammad A.

2014-05-01

Glucokinase (GK) is involved in normal glucose homeostasis and therefore it is a valid target for drug design and discovery efforts. GK activators (GKAs) have excellent potential as treatments of hyperglycemia and diabetes. The combined recent interest in GKAs, together with docking limitations and shortages of docking validation methods prompted us to use our new 3D-QSAR analysis, namely, docking-based comparative intermolecular contacts analysis (dbCICA), to validate docking configurations performed on a group of GKAs within GK binding site. dbCICA assesses the consistency of docking by assessing the correlation between ligands' affinities and their contacts with binding site spots. Optimal dbCICA models were validated by receiver operating characteristic curve analysis and comparative molecular field analysis. dbCICA models were also converted into valid pharmacophores that were used as search queries to mine 3D structural databases for new GKAs. The search yielded several potent bioactivators that experimentally increased GK bioactivity up to 7.5-folds at 10 μM.

Expedition 27 Docking

NASA Image and Video Library

2011-04-06

Russian Mission Control Center is seen on Thursday, April 7, 2011 in Korolev, Russia. The Soyuz TMA-21 docked to the International Space Station carrying Expedition 27 Soyuz Commander Alexander Samokutyaev, NASA Flight Engineer Ron Garan and Russian Flight Engineer Andrey Borisenko. Photo Credit: (NASA/Carla Cioffi)

Predicting the Accuracy of Protein–Ligand Docking on Homology Models

PubMed Central

BORDOGNA, ANNALISA; PANDINI, ALESSANDRO; BONATI, LAURA

2011-01-01

Ligand–protein docking is increasingly used in Drug Discovery. The initial limitations imposed by a reduced availability of target protein structures have been overcome by the use of theoretical models, especially those derived by homology modeling techniques. While this greatly extended the use of docking simulations, it also introduced the need for general and robust criteria to estimate the reliability of docking results given the model quality. To this end, a large-scale experiment was performed on a diverse set including experimental structures and homology models for a group of representative ligand–protein complexes. A wide spectrum of model quality was sampled using templates at different evolutionary distances and different strategies for target–template alignment and modeling. The obtained models were scored by a selection of the most used model quality indices. The binding geometries were generated using AutoDock, one of the most common docking programs. An important result of this study is that indeed quantitative and robust correlations exist between the accuracy of docking results and the model quality, especially in the binding site. Moreover, state-of-the-art indices for model quality assessment are already an effective tool for an a priori prediction of the accuracy of docking experiments in the context of groups of proteins with conserved structural characteristics. PMID:20607693

33 CFR 110.130 - Bar Harbor, Maine.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Bar Harbor, Maine. 110.130... ANCHORAGE REGULATIONS Anchorage Grounds § 110.130 Bar Harbor, Maine. (a) Anchorage grounds. (1) Anchorage “A” is that portion of Frenchman Bay, Bar Harbor, ME enclosed by a rhumb line connecting the following...

Developing a cross-docking network design model under uncertain environment

NASA Astrophysics Data System (ADS)

Seyedhoseini, S. M.; Rashid, Reza; Teimoury, E.

2015-06-01

Cross-docking is a logistic concept, which plays an important role in supply chain management by decreasing inventory holding, order packing, transportation costs and delivery time. Paying attention to these concerns, and importance of the congestion in cross docks, we present a mixed-integer model to optimize the location and design of cross docks at the same time to minimize the total transportation and operating costs. The model combines queuing theory for design aspects, for that matter, we consider a network of cross docks and customers where two M/M/c queues have been represented to describe operations of indoor trucks and outdoor trucks in each cross dock. To prepare a perfect illustration for performance of the model, a real case also has been examined that indicated effectiveness of the proposed model.

Overview of LIDS Docking and Berthing System Seals

NASA Technical Reports Server (NTRS)

Daniels, Christopher C.; Dunlap, Patrick H., Jr.; deGroh, Henry C., III; Steinetz, Bruce M.; Oswald, Jay J.; Smith, Ian

2007-01-01

This viewgraph presentation describes the Low Impact Docking System (LIDS) docking and berthing system seals. The contents include: 1) Description of the Application: Low Impact Docking System (LIDS); 2) LIDS Seal Locations: Vehicle Undocked (Hatch Closed); 3) LIDS Seal Locations: Mechanical Pass Thru; 4) LIDS Seal Locations: Electrical and Pyro Connectors; 5) LIDS Seal Locations: Vehicle Docked (Hatches Open); 6) LIDS Seal Locations: Main Interface Seal; 7) Main Interface Seal Challenges and Specifications; 8) Approach; 9) Seal Concepts Under Development/Evaluation; 10) Elastomer Material Evaluations; 11) Evaluation of Relevant Seal Properties; 12) Medium-Scale (12") Gask-O-Seal Compression Tests; 13) Medium-Scale Compression Results; 14) Adhesion Forces of Elliptical Top Gask-o-seals; 15) Medium-Scale Seals; 16) Medium-Scale Leakage Results: Effect of Configuration; 17) Full Scale LIDS Seal Test Rig Development; 18) Materials International Space Station Experiment (MISSE 6A and 6B); and 19) Schedule.

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

PubMed Central

Fang, Ye; Ding, Yun; Feinstein, Wei P.; Koppelman, David M.; Moreno, Juana; Jarrell, Mark; Ramanujam, J.; Brylinski, Michal

2016-01-01

Computational modeling of drug binding to proteins is an integral component of direct drug design. Particularly, structure-based virtual screening is often used to perform large-scale modeling of putative associations between small organic molecules and their pharmacologically relevant protein targets. Because of a large number of drug candidates to be evaluated, an accurate and fast docking engine is a critical element of virtual screening. Consequently, highly optimized docking codes are of paramount importance for the effectiveness of virtual screening methods. In this communication, we describe the implementation, tuning and performance characteristics of GeauxDock, a recently developed molecular docking program. GeauxDock is built upon the Monte Carlo algorithm and features a novel scoring function combining physics-based energy terms with statistical and knowledge-based potentials. Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU). First, we carried out a thorough performance tuning of the high-level framework and the docking kernel to produce a fast serial code, which was then ported to shared-memory multi-core CPUs yielding a near-ideal scaling. Further, using Xeon Phi gives 1.9× performance improvement over a dual 10-core Xeon CPU, whereas the best GPU accelerator, GeForce GTX 980, achieves a speedup as high as 3.5×. On that account, GeauxDock can take advantage of modern heterogeneous architectures to considerably accelerate structure-based virtual screening applications. GeauxDock is open-sourced and publicly available at www.brylinski.org/geauxdock and https://figshare.com/articles/geauxdock_tar_gz/3205249. PMID:27420300

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing.

PubMed

Fang, Ye; Ding, Yun; Feinstein, Wei P; Koppelman, David M; Moreno, Juana; Jarrell, Mark; Ramanujam, J; Brylinski, Michal

2016-01-01

Computational modeling of drug binding to proteins is an integral component of direct drug design. Particularly, structure-based virtual screening is often used to perform large-scale modeling of putative associations between small organic molecules and their pharmacologically relevant protein targets. Because of a large number of drug candidates to be evaluated, an accurate and fast docking engine is a critical element of virtual screening. Consequently, highly optimized docking codes are of paramount importance for the effectiveness of virtual screening methods. In this communication, we describe the implementation, tuning and performance characteristics of GeauxDock, a recently developed molecular docking program. GeauxDock is built upon the Monte Carlo algorithm and features a novel scoring function combining physics-based energy terms with statistical and knowledge-based potentials. Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU). First, we carried out a thorough performance tuning of the high-level framework and the docking kernel to produce a fast serial code, which was then ported to shared-memory multi-core CPUs yielding a near-ideal scaling. Further, using Xeon Phi gives 1.9× performance improvement over a dual 10-core Xeon CPU, whereas the best GPU accelerator, GeForce GTX 980, achieves a speedup as high as 3.5×. On that account, GeauxDock can take advantage of modern heterogeneous architectures to considerably accelerate structure-based virtual screening applications. GeauxDock is open-sourced and publicly available at www.brylinski.org/geauxdock and https://figshare.com/articles/geauxdock_tar_gz/3205249.

Protein-Protein Docking in Drug Design and Discovery.

PubMed

Kaczor, Agnieszka A; Bartuzi, Damian; Stępniewski, Tomasz Maciej; Matosiuk, Dariusz; Selent, Jana

2018-01-01

Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.

PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking.

PubMed

Ng, Marcus C K; Fong, Simon; Siu, Shirley W I

2015-06-01

Protein-ligand docking is an essential step in modern drug discovery process. The challenge here is to accurately predict and efficiently optimize the position and orientation of ligands in the binding pocket of a target protein. In this paper, we present a new method called PSOVina which combined the particle swarm optimization (PSO) algorithm with the efficient Broyden-Fletcher-Goldfarb-Shannon (BFGS) local search method adopted in AutoDock Vina to tackle the conformational search problem in docking. Using a diverse data set of 201 protein-ligand complexes from the PDBbind database and a full set of ligands and decoys for four representative targets from the directory of useful decoys (DUD) virtual screening data set, we assessed the docking performance of PSOVina in comparison to the original Vina program. Our results showed that PSOVina achieves a remarkable execution time reduction of 51-60% without compromising the prediction accuracies in the docking and virtual screening experiments. This improvement in time efficiency makes PSOVina a better choice of a docking tool in large-scale protein-ligand docking applications. Our work lays the foundation for the future development of swarm-based algorithms in molecular docking programs. PSOVina is freely available to non-commercial users at http://cbbio.cis.umac.mo .

33 CFR 110.9 - Wells Harbor, Maine.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Wells Harbor, Maine. 110.9... ANCHORAGE REGULATIONS Special Anchorage Areas § 110.9 Wells Harbor, Maine. (a) Anchorage “A”. All of the... approximately 5,800 sq. yards, encompassing the central portion of Wells Harbor. (b) Anchorage “B”. All of the...

33 CFR 110.9 - Wells Harbor, Maine.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Wells Harbor, Maine. 110.9... ANCHORAGE REGULATIONS Special Anchorage Areas § 110.9 Wells Harbor, Maine. Link to an amendment published at..., encompassing the central portion of Wells Harbor. (b) Anchorage “B”. All of the waters enclosed by a line...

ATV docking ops

NASA Image and Video Library

2014-08-12

ISS040-E-091634 (12 Aug. 2014) --- In the Zvezda Service Module, European Space Agency astronaut Alexander Gerst (left) and Russian cosmonaut Alexander Skvortsov, both Expedition 40 flight engineers, monitor the approach and docking of ESA's "Georges Lemaitre" Automated Transfer Vehicle-5 (ATV-5) to the International Space Station.

ATV docking ops

NASA Image and Video Library

2014-08-12

ISS040-E-091638 (12 Aug. 2014) --- In the Zvezda Service Module, European Space Agency astronaut Alexander Gerst (left) and Russian cosmonaut Alexander Skvortsov, both Expedition 40 flight engineers, monitor the approach and docking of ESA's "Georges Lemaitre" Automated Transfer Vehicle-5 (ATV-5) to the International Space Station.

ATV docking ops

NASA Image and Video Library

2014-08-12

ISS040-E-091635 (12 Aug. 2014) --- In the Zvezda Service Module, European Space Agency astronaut Alexander Gerst (left) and Russian cosmonaut Alexander Skvortsov, both Expedition 40 flight engineers, monitor the approach and docking of ESA's "Georges Lemaitre" Automated Transfer Vehicle-5 (ATV-5) to the International Space Station.

ATV docking ops

NASA Image and Video Library

2014-08-12

ISS040-E-091655 (12 Aug. 2014) --- In the Zvezda Service Module, European Space Agency astronaut Alexander Gerst (right) and Russian cosmonaut Alexander Skvortsov, both Expedition 40 flight engineers, monitor the approach and docking of ESA's "Georges Lemaitre" Automated Transfer Vehicle-5 (ATV-5) to the International Space Station.

33 CFR 207.610 - St. Lawrence River, Cape Vincent Harbor, N.Y.; use, administration, and navigation of the harbor...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false St. Lawrence River, Cape Vincent Harbor, N.Y.; use, administration, and navigation of the harbor and U.S. breakwater. 207.610 Section 207... NAVIGATION REGULATIONS § 207.610 St. Lawrence River, Cape Vincent Harbor, N.Y.; use, administration, and...

Template-based protein-protein docking exploiting pairwise interfacial residue restraints.

PubMed

Xue, Li C; Rodrigues, João P G L M; Dobbs, Drena; Honavar, Vasant; Bonvin, Alexandre M J J

2017-05-01

Although many advanced and sophisticated ab initio approaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to exploit template information in the modeling process. Here, we systematically evaluate and benchmark a TBM method that uses conserved interfacial residue pairs as docking distance restraints [referred to as alpha carbon-alpha carbon (CA-CA)-guided docking]. We compare it with two other template-based protein-protein modeling approaches, including a conserved non-pairwise interfacial residue restrained docking approach [referred to as the ambiguous interaction restraint (AIR)-guided docking] and a simple superposition-based modeling approach. Our results show that, for most cases, the CA-CA-guided docking method outperforms both superposition with refinement and the AIR-guided docking method. We emphasize the superiority of the CA-CA-guided docking on cases with medium to large conformational changes, and interactions mediated through loops, tails or disordered regions. Our results also underscore the importance of a proper refinement of superimposition models to reduce steric clashes. In summary, we provide a benchmarked TBM protocol that uses conserved pairwise interface distance as restraints in generating realistic 3D protein-protein interaction models, when reliable templates are available. The described CA-CA-guided docking protocol is based on the HADDOCK platform, which allows users to incorporate additional prior knowledge of the target system to further improve the quality of the resulting models. © The Author 2016. Published by Oxford University Press.

Molecular Docking Study on Galantamine Derivatives as Cholinesterase Inhibitors.

PubMed

Atanasova, Mariyana; Yordanov, Nikola; Dimitrov, Ivan; Berkov, Strahil; Doytchinova, Irini

2015-06-01

A training set of 22 synthetic galantamine derivatives binding to acetylcholinesterase was docked by GOLD and the protocol was optimized in terms of scoring function, rigidity/flexibility of the binding site, presence/absence of a water molecule inside and radius of the binding site. A moderate correlation was found between the affinities of compounds expressed as pIC50 values and their docking scores. The optimized docking protocol was validated by an external test set of 11 natural galantamine derivatives and the correlation coefficient between the docking scores and the pIC50 values was 0.800. The derived relationship was used to analyze the interactions between galantamine derivatives and AChE. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

33 CFR 117.272 - Boot Key Harbor.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Boot Key Harbor. 117.272 Section 117.272 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Florida § 117.272 Boot Key Harbor. The draw of the Boot Key Harbor drawbridge, mile 0.13, between...

Defense.gov Special Report: Pearl Harbor Anniversary

Science.gov Websites

Department of Defense Submit Search 71th Anniversary of the Attack on Pearl Harbor - World War II News Joint Chiefs of Staff, saluted veterans at the National World War II Memorial in Washington, D.C Attack Video Return To Pearl Harbor Return To Pearl Harbor World War II Timeline The attack on Pearl

International Docking Standard (IDSS) Interface Definition Document (IDD) . E; Revision

NASA Technical Reports Server (NTRS)

Kelly, Sean M.; Cryan, Scott P.

2016-01-01

This International Docking System Standard (IDSS) Interface Definition Document (IDD) is the result of a collaboration by the International Space Station membership to establish a standard docking interface to enable on-orbit crew rescue operations and joint collaborative endeavors utilizing different spacecraft. This IDSS IDD details the physical geometric mating interface and design loads requirements. The physical geometric interface requirements must be strictly followed to ensure physical spacecraft mating compatibility. This includes both defined components and areas that are void of components. The IDD also identifies common design parameters as identified in section 3.0, e.g., docking initial conditions and vehicle mass properties. This information represents a recommended set of design values enveloping a broad set of design reference missions and conditions, which if accommodated in the docking system design, increases the probability of successful docking between different spacecraft. This IDD does not address operational procedures or off-nominal situations, nor does it dictate implementation or design features behind the mating interface. It is the responsibility of the spacecraft developer to perform all hardware verification and validation, and to perform final docking analyses to ensure the needed docking performance and to develop the final certification loads for their application. While there are many other critical requirements needed in the development of a docking system such as fault tolerance, reliability, and environments (e.g. vibration, etc.), it is not the intent of the IDSS IDD to mandate all of these requirements; these requirements must be addressed as part of the specific developer's unique program, spacecraft and mission needs. This approach allows designers the flexibility to design and build docking mechanisms to their unique program needs and requirements. The purpose of the IDSS IDD is to provide basic common design parameters

Geoscience rediscovers Phoenicia's buried harbors

NASA Astrophysics Data System (ADS)

Marriner, Nick; Morhange, Christophe; Doumet-Serhal, Claude; Carbonel, Pierre

2006-01-01

After centuries of archaeological debate, the harbors of Phoenicia's two most important city states, Tyre and Sidon, have been rediscovered, and including new geoarcheological results reveal how, where, and when they evolved after their Bronze Age foundations. The early ports lie beneath their present urban centers, and we have indentified four harbor phases. (1) During the Bronze Age, Tyre and Sidon were characterized by semi-open marine coves that served as protoharbors. (2) Biostratigraphic and lithostratigraphic data indicate the presence of early artificial basins after the first millennium B.C. (3) The harbors reached their apogees during the Greco-Roman and Byzantine periods. (4) Silting up and coastal progradation led to burial of the medieval basins, lost until now.

DOCK8 regulates lymphocyte shape integrity for skin antiviral immunity

PubMed Central

Zhang, Qian; Dove, Christopher G.; Hor, Jyh Liang; Murdock, Heardley M.; Strauss-Albee, Dara M.; Garcia, Jordan A.; Mandl, Judith N.; Grodick, Rachael A.; Jing, Huie; Chandler-Brown, Devon B.; Lenardo, Timothy E.; Crawford, Greg; Matthews, Helen F.; Freeman, Alexandra F.; Cornall, Richard J.; Germain, Ronald N.

2014-01-01

DOCK8 mutations result in an inherited combined immunodeficiency characterized by increased susceptibility to skin and other infections. We show that when DOCK8-deficient T and NK cells migrate through confined spaces, they develop cell shape and nuclear deformation abnormalities that do not impair chemotaxis but contribute to a distinct form of catastrophic cell death we term cytothripsis. Such defects arise during lymphocyte migration in collagen-dense tissues when DOCK8, through CDC42 and p21-activated kinase (PAK), is unavailable to coordinate cytoskeletal structures. Cytothripsis of DOCK8-deficient cells prevents the generation of long-lived skin-resident memory CD8 T cells, which in turn impairs control of herpesvirus skin infections. Our results establish that DOCK8-regulated shape integrity of lymphocytes prevents cytothripsis and promotes antiviral immunity in the skin. PMID:25422492

ATV docking ops

NASA Image and Video Library

2014-08-12

ISS040-E-091688 (12 Aug. 2014) --- In the Zvezda Service Module, European Space Agency astronaut Alexander Gerst (left) and Russian cosmonaut Alexander Skvortsov, both Expedition 40 flight engineers, monitor the approach and docking of ESA?s "Georges Lemaitre" Automated Transfer Vehicle-5 (ATV-5) to the International Space Station.

Virtual Screening with AutoDock: Theory and Practice

PubMed Central

Cosconati, Sandro; Forli, Stefano; Perryman, Alex L.; Harris, Rodney; Goodsell, David S.; Olson, Arthur J.

2011-01-01

Importance to the field Virtual screening is a computer-based technique for identifying promising compounds to bind to a target molecule of known structure. Given the rapidly increasing number of protein and nucleic acid structures, virtual screening continues to grow as an effective method for the discovery of new inhibitors and drug molecules. Areas covered in this review We describe virtual screening methods that are available in the AutoDock suite of programs, and several of our successes in using AutoDock virtual screening in pharmaceutical lead discovery. What the reader will gain A general overview of the challenges of virtual screening is presented, along with the tools available in the AutoDock suite of programs for addressing these challenges. Take home message Virtual screening is an effective tool for the discovery of compounds for use as leads in drug discovery, and the free, open source program AutoDock is an effective tool for virtual screening. PMID:21532931

Dezhurov removes the docking probe in Zvezda during Expedition Three

NASA Image and Video Library

2001-09-17

ISS003-E-5621 (17 September 2001) --- Cosmonaut Vladimir Dezhurov, Expedition Three flight engineer, prepares to remove the docking probe in the Zvezda Service Module's pressurized adapter. The docking probe successfully guided the arrival of the Russian-built Pirs docking compartment to the International Space Station (ISS). Mikhail Tyurin, flight engineer, is visible in the background. Tyurin and Dezhurov represent Rosaviakosmos.

Ensemble-based docking: From hit discovery to metabolism and toxicity predictions.

PubMed

Evangelista, Wilfredo; Weir, Rebecca L; Ellingson, Sally R; Harris, Jason B; Kapoor, Karan; Smith, Jeremy C; Baudry, Jerome

2016-10-15

This paper describes and illustrates the use of ensemble-based docking, i.e., using a collection of protein structures in docking calculations for hit discovery, the exploration of biochemical pathways and toxicity prediction of drug candidates. We describe the computational engineering work necessary to enable large ensemble docking campaigns on supercomputers. We show examples where ensemble-based docking has significantly increased the number and the diversity of validated drug candidates. Finally, we illustrate how ensemble-based docking can be extended beyond hit discovery and toward providing a structural basis for the prediction of metabolism and off-target binding relevant to pre-clinical and clinical trials. Copyright © 2016 Elsevier Ltd. All rights reserved.

Terminal Homing for Autonomous Underwater Vehicle Docking

DTIC Science & Technology

2016-06-01

underwater domain, accurate navigation. Above the water, light and electromagnetic signals travel well through air and space, mediums that allow for a...DISTRIBUTION CODE 13. ABSTRACT The use of docking stations for autonomous underwater vehicles (AUV) provides the ability to keep a vehicle on...Mechanical and Aerospace Engineering iv THIS PAGE INTENTIONALLY LEFT BLANK v ABSTRACT The use of docking stations for autonomous underwater

GEMINI-TITAN (GT)-11 - EARTH - SKY - DOCKING - OUTER SPACE

NASA Image and Video Library

1966-07-18

S66-46144 (18 July 1966) --- The Gemini-10 spacecraft is successfully docked with the Agena Target Docking Vehicle 5005. The Agena display panel is clearly visible. After docking with the Agena, astronauts John W. Young, command pilot, and Michael Collins, pilot, fired the 16,000-pound thrust engine of Agena-10's primary propulsion system to boost the combined vehicles into an orbit with an apogee of 413 nautical miles to set a new altitude record for manned spaceflight. Photo credit: NASA

Protein-ligand docking with multiple flexible side chains

NASA Astrophysics Data System (ADS)

Zhao, Yong; Sanner, Michel F.

2008-09-01

In this work, we validate and analyze the results of previously published cross docking experiments and classify failed dockings based on the conformational changes observed in the receptors. We show that a majority of failed experiments (i.e. 25 out of 33, involving four different receptors: cAPK, CDK2, Ricin and HIVp) are due to conformational changes in side chains near the active site. For these cases, we identify the side chains to be made flexible during docking calculation by superimposing receptors and analyzing steric overlap between various ligands and receptor side chains. We demonstrate that allowing these side chains to assume rotameric conformations enables the successful cross docking of 19 complexes (ligand all atom RMSD < 2.0 Å) using our docking software FLIPDock. The number of side receptor side chains interacting with a ligand can vary according to the ligand's size and shape. Hence, when starting from a complex with a particular ligand one might have to extend the region of potential interacting side chains beyond the ones interacting with the known ligand. We discuss distance-based methods for selecting additional side chains in the neighborhood of the known active site. We show that while using the molecular surface to grow the neighborhood is more efficient than Euclidian-distance selection, the number of side chains selected by these methods often remains too large and additional methods for reducing their count are needed. Despite these difficulties, using geometric constraints obtained from the network of bonded and non-bonded interactions to rank residues and allowing the top ranked side chains to be flexible during docking makes 22 out of 25 complexes successful.

Apollo-Soyuz test project docking system

NASA Technical Reports Server (NTRS)

Swan, W. L., Jr.

1976-01-01

The United States and Soviet Union in July 1975 successfully completed a joint space mission utilizing each country's spacecraft and the compatible docking system designed and fabricated by each country. The compatible docking system is described, along with the extensive research, development, and testing leading up to the successful mission. It also describes the formulation and implementation of methods for breaking the language barrier, bridging the extensive distances for communication and travel, and adjusting to each country's different culture during the three-year development program.

Vision Based Navigation for Autonomous Cooperative Docking of CubeSats

NASA Astrophysics Data System (ADS)

Pirat, Camille; Ankersen, Finn; Walker, Roger; Gass, Volker

2018-05-01

A realistic rendezvous and docking navigation solution applicable to CubeSats is investigated. The scalability analysis of the ESA Autonomous Transfer Vehicle Guidance, Navigation & Control (GNC) performances and the Russian docking system, shows that the docking of two CubeSats would require a lateral control performance of the order of 1 cm. Line of sight constraints and multipath effects affecting Global Navigation Satellite System (GNSS) measurements in close proximity prevent the use of this sensor for the final approach. This consideration and the high control accuracy requirement led to the use of vision sensors for the final 10 m of the rendezvous and docking sequence. A single monocular camera on the chaser satellite and various sets of Light-Emitting Diodes (LEDs) on the target vehicle ensure the observability of the system throughout the approach trajectory. The simple and novel formulation of the measurement equations allows differentiating unambiguously rotations from translations between the target and chaser docking port and allows a navigation performance better than 1 mm at docking. Furthermore, the non-linear measurement equations can be solved in order to provide an analytic navigation solution. This solution can be used to monitor the navigation filter solution and ensure its stability, adding an extra layer of robustness for autonomous rendezvous and docking. The navigation filter initialization is addressed in detail. The proposed method is able to differentiate LEDs signals from Sun reflections as demonstrated by experimental data. The navigation filter uses a comprehensive linearised coupled rotation/translation dynamics, describing the chaser to target docking port motion. The handover, between GNSS and vision sensor measurements, is assessed. The performances of the navigation function along the approach trajectory is discussed.

Tyurin packs the docking probe in Node 1 during Expedition Three

NASA Image and Video Library

2001-09-17

ISS003-E-5634 (17 September 2001) --- Cosmonaut Mikhail Tyurin, Expedition Three flight engineer, packs the docking probe in a stowage bag in Unity. The docking probe successfully guided the arrival of the Russian-built Pirs docking compartment to the International Space Station (ISS). Tyurin represents Rosaviakosmos.

Remote operation of an orbital maneuvering vehicle in simulated docking maneuvers

NASA Technical Reports Server (NTRS)

Brody, Adam R.

1990-01-01

Simulated docking maneuvers were performed to assess the effect of initial velocity on docking failure rate, mission duration, and delta v (fuel consumption). Subjects performed simulated docking maneuvers of an orbital maneuvering vehicle (OMV) to a space station. The effect of the removal of the range and rate displays (simulating a ranging instrumentation failure) was also examined. Naive subjects were capable of achieving a high success rate in performing simulated docking maneuvers without extensive training. Failure rate was a function of individual differences; there was no treatment effect on failure rate. The amount of time subjects reserved for final approach increased with starting velocity. Piloting of docking maneuvers was not significantly affected in any way by the removal of range and rate displays. Radial impulse was significant both by subject and by treatment. NASA's 0.1 percent rule, dictating an approach rate no greater than 0.1 percent of the range, is seen to be overly conservative for nominal docking missions.

jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework.

PubMed

López-Camacho, Esteban; García Godoy, María Jesús; Nebro, Antonio J; Aldana-Montes, José F

2014-02-01

Molecular docking is a method for structure-based drug design and structural molecular biology, which attempts to predict the position and orientation of a small molecule (ligand) in relation to a protein (receptor) to produce a stable complex with a minimum binding energy. One of the most widely used software packages for this purpose is AutoDock, which incorporates three metaheuristic techniques. We propose the integration of AutoDock with jMetalCpp, an optimization framework, thereby providing both single- and multi-objective algorithms that can be used to effectively solve docking problems. The resulting combination of AutoDock + jMetalCpp allows users of the former to easily use the metaheuristics provided by the latter. In this way, biologists have at their disposal a richer set of optimization techniques than those already provided in AutoDock. Moreover, designers of metaheuristic techniques can use molecular docking for case studies, which can lead to more efficient algorithms oriented to solving the target problems.  jMetalCpp software adapted to AutoDock is freely available as a C++ source code at http://khaos.uma.es/AutodockjMetal/.

Machine Vision for Relative Spacecraft Navigation During Approach to Docking

NASA Technical Reports Server (NTRS)

Chien, Chiun-Hong; Baker, Kenneth

2011-01-01

This paper describes a machine vision system for relative spacecraft navigation during the terminal phase of approach to docking that: 1) matches high contrast image features of the target vehicle, as seen by a camera that is bore-sighted to the docking adapter on the chase vehicle, to the corresponding features in a 3d model of the docking adapter on the target vehicle and 2) is robust to on-orbit lighting. An implementation is provided for the case of the Space Shuttle Orbiter docking to the International Space Station (ISS) with quantitative test results using a full scale, medium fidelity mock-up of the ISS docking adapter mounted on a 6-DOF motion platform at the NASA Marshall Spaceflight Center Flight Robotics Laboratory and qualitative test results using recorded video from the Orbiter Docking System Camera (ODSC) during multiple orbiter to ISS docking missions. The Natural Feature Image Registration (NFIR) system consists of two modules: 1) Tracking which tracks the target object from image to image and estimates the position and orientation (pose) of the docking camera relative to the target object and 2) Acquisition which recognizes the target object if it is in the docking camera Field-of-View and provides an approximate pose that is used to initialize tracking. Detected image edges are matched to the 3d model edges whose predicted location, based on the pose estimate and its first time derivative from the previous frame, is closest to the detected edge1 . Mismatches are eliminated using a rigid motion constraint. The remaining 2d image to 3d model matches are used to make a least squares estimate of the change in relative pose from the previous image to the current image. The changes in position and in attitude are used as data for two Kalman filters whose outputs are smoothed estimate of position and velocity plus attitude and attitude rate that are then used to predict the location of the 3d model features in the next image.

Autonomous docking ground demonstration (category 3)

NASA Technical Reports Server (NTRS)

Lamkin, Steve L.; Eick, Richard E.; Baxter, James M.; Boyd, M. G.; Clark, Fred D.; Lee, Thomas Q.; Othon, L. T.; Prather, Joseph L.; Spehar, Peter T.; Teders, Rebecca J.

1991-01-01

The NASA Johnson Space Center (JSC) is involved in the development of an autonomous docking ground demonstration. The demonstration combines the technologies, expertise and facilities of the JSC Tracking and Communications Division (EE), Structures and Mechanics Division (ES), and the Navigation, Guidance and Control Division (EG) and their supporting contractors. The autonomous docking ground demonstration is an evaluation of the capabilities of the laser sensor system to support the docking phase (12ft to contact) when operated in conjunction with the Guidance, Navigation and Control Software. The docking mechanism being used was developed for the Apollo Soyuz Test Program. This demonstration will be conducted using the Six-Degrees of Freedom (6-DOF) Dynamic Test System (DTS). The DTS environment simulates the Space Station Freedom as the stationary or target vehicle and the Orbiter as the active or chase vehicle. For this demonstration the laser sensor will be mounted on the target vehicle and the retroreflectors on the chase vehicle. This arrangement was used to prevent potential damage to the laser. The sensor system. GN&C and 6-DOF DTS will be operated closed-loop. Initial condition to simulate vehicle misalignments, translational and rotational, will be introduced within the constraints of the systems involved. Detailed description of each of the demonstration components (e.g., Sensor System, GN&C, 6-DOF DTS and supporting computer configuration) including their capabilities and limitations will be discussed. A demonstration architecture drawing and photographs of the test configuration will be presented.

Autonomous docking ground demonstration (category 3)

NASA Astrophysics Data System (ADS)

Lamkin, Steve L.; Eick, Richard E.; Baxter, James M.; Boyd, M. G.; Clark, Fred D.; Lee, Thomas Q.; Othon, L. T.; Prather, Joseph L.; Spehar, Peter T.; Teders, Rebecca J.

The NASA Johnson Space Center (JSC) is involved in the development of an autonomous docking ground demonstration. The demonstration combines the technologies, expertise and facilities of the JSC Tracking and Communications Division (EE), Structures and Mechanics Division (ES), and the Navigation, Guidance and Control Division (EG) and their supporting contractors. The autonomous docking ground demonstration is an evaluation of the capabilities of the laser sensor system to support the docking phase (12ft to contact) when operated in conjunction with the Guidance, Navigation and Control Software. The docking mechanism being used was developed for the Apollo Soyuz Test Program. This demonstration will be conducted using the Six-Degrees of Freedom (6-DOF) Dynamic Test System (DTS). The DTS environment simulates the Space Station Freedom as the stationary or target vehicle and the Orbiter as the active or chase vehicle. For this demonstration the laser sensor will be mounted on the target vehicle and the retroreflectors on the chase vehicle. This arrangement was used to prevent potential damage to the laser. The sensor system. GN&C and 6-DOF DTS will be operated closed-loop. Initial condition to simulate vehicle misalignments, translational and rotational, will be introduced within the constraints of the systems involved. Detailed description of each of the demonstration components (e.g., Sensor System, GN&C, 6-DOF DTS and supporting computer configuration) including their capabilities and limitations will be discussed. A demonstration architecture drawing and photographs of the test configuration will be presented.

Pharmacophore-Based Similarity Scoring for DOCK

PubMed Central

2015-01-01

Pharmacophore modeling incorporates geometric and chemical features of known inhibitors and/or targeted binding sites to rationally identify and design new drug leads. In this study, we have encoded a three-dimensional pharmacophore matching similarity (FMS) scoring function into the structure-based design program DOCK. Validation and characterization of the method are presented through pose reproduction, crossdocking, and enrichment studies. When used alone, FMS scoring dramatically improves pose reproduction success to 93.5% (∼20% increase) and reduces sampling failures to 3.7% (∼6% drop) compared to the standard energy score (SGE) across 1043 protein–ligand complexes. The combined FMS+SGE function further improves success to 98.3%. Crossdocking experiments using FMS and FMS+SGE scoring, for six diverse protein families, similarly showed improvements in success, provided proper pharmacophore references are employed. For enrichment, incorporating pharmacophores during sampling and scoring, in most cases, also yield improved outcomes when docking and rank-ordering libraries of known actives and decoys to 15 systems. Retrospective analyses of virtual screenings to three clinical drug targets (EGFR, IGF-1R, and HIVgp41) using X-ray structures of known inhibitors as pharmacophore references are also reported, including a customized FMS scoring protocol to bias on selected regions in the reference. Overall, the results and fundamental insights gained from this study should benefit the docking community in general, particularly researchers using the new FMS method to guide computational drug discovery with DOCK. PMID:25229837

GRAMM-X public web server for protein–protein docking

PubMed Central

Tovchigrechko, Andrey; Vakser, Ilya A.

2006-01-01

Protein docking software GRAMM-X and its web interface () extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track. PMID:16845016

78 FR 38577 - Special Local Regulations; Red Bull Flugtag National Harbor Event, Potomac River; National Harbor...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-27

...-AA08 Special Local Regulations; Red Bull Flugtag National Harbor Event, Potomac River; National Harbor... waters of the Potomac River on September 21, 2013. These special local regulations are necessary to... temporarily restrict vessel traffic in a portion of the Potomac River during the event. DATES: This rule is...

Rendezvous and docking tracker

NASA Technical Reports Server (NTRS)

Ray, Art J.; Ross, Susan E.; Deming, Douglas R.

1986-01-01

A conceptual solid-state rendezvous and docking tracker (RDT) has been devised for generating range and attitude data for a docking vehicle relative to a target vehicle. Emphasis is placed on the approach of the Orbiter to a link with the Space Station. Three laser illuminators ring the optical axis of the lens a directed toward retroreflectors on the target vehicle. Each retroreflector is equipped with a bandpass filter for a designated illumination frequency. Data are collected sequentially over a 20 deg field of view as the range closes to 100-1000 m. A fourth ranging retroreflector 0.3 m from center is employed during close-in maneuvers. The system provides tracking data on motions with 6 deg of freedom, and furnishes 500 msec updates (to be enhanced to 100 msec) to the operator at a computer console.

A dynamic motion simulator for future European docking systems

NASA Technical Reports Server (NTRS)

Brondino, G.; Marchal, PH.; Grimbert, D.; Noirault, P.

1990-01-01

Europe's first confrontation with docking in space will require extensive testing to verify design and performance and to qualify hardware. For this purpose, a Docking Dynamics Test Facility (DDTF) was developed. It allows reproduction on the ground of the same impact loads and relative motion dynamics which would occur in space during docking. It uses a 9 degree of freedom, servo-motion system, controlled by a real time computer, which simulates the docking spacecraft in a zero-g environment. The test technique involves and active loop based on six axis force and torque detection, a mathematical simulation of individual spacecraft dynamics, and a 9 degree of freedom servomotion of which 3 DOFs allow extension of the kinematic range to 5 m. The configuration was checked out by closed loop tests involving spacecraft control models and real sensor hardware. The test facility at present has an extensive configuration that allows evaluation of both proximity control and docking systems. It provides a versatile tool to verify system design, hardware items and performance capabilities in the ongoing HERMES and COLUMBUS programs. The test system is described and its capabilities are summarized.

78 FR 18274 - Special Local Regulations; Red Bull Flugtag National Harbor Event, Potomac River; National Harbor...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-26

...-AA08 Special Local Regulations; Red Bull Flugtag National Harbor Event, Potomac River; National Harbor... event,'' to be held on the waters of the Potomac River on September 21, 2013. These special local... representative. This action is intended to temporarily restrict vessel traffic in a portion of the Potomac River...

A High Performance Cloud-Based Protein-Ligand Docking Prediction Algorithm

PubMed Central

Chen, Jui-Le; Yang, Chu-Sing

2013-01-01

The potential of predicting druggability for a particular disease by integrating biological and computer science technologies has witnessed success in recent years. Although the computer science technologies can be used to reduce the costs of the pharmaceutical research, the computation time of the structure-based protein-ligand docking prediction is still unsatisfied until now. Hence, in this paper, a novel docking prediction algorithm, named fast cloud-based protein-ligand docking prediction algorithm (FCPLDPA), is presented to accelerate the docking prediction algorithm. The proposed algorithm works by leveraging two high-performance operators: (1) the novel migration (information exchange) operator is designed specially for cloud-based environments to reduce the computation time; (2) the efficient operator is aimed at filtering out the worst search directions. Our simulation results illustrate that the proposed method outperforms the other docking algorithms compared in this paper in terms of both the computation time and the quality of the end result. PMID:23762864

Autonomous Vision-Based Tethered-Assisted Rover Docking

NASA Technical Reports Server (NTRS)

Tsai, Dorian; Nesnas, Issa A.D.; Zarzhitsky, Dimitri

2013-01-01

Many intriguing science discoveries on planetary surfaces, such as the seasonal flows on crater walls and skylight entrances to lava tubes, are at sites that are currently inaccessible to state-of-the-art rovers. The in situ exploration of such sites is likely to require a tethered platform both for mechanical support and for providing power and communication. Mother/daughter architectures have been investigated where a mother deploys a tethered daughter into extreme terrains. Deploying and retracting a tethered daughter requires undocking and re-docking of the daughter to the mother, with the latter being the challenging part. In this paper, we describe a vision-based tether-assisted algorithm for the autonomous re-docking of a daughter to its mother following an extreme terrain excursion. The algorithm uses fiducials mounted on the mother to improve the reliability and accuracy of estimating the pose of the mother relative to the daughter. The tether that is anchored by the mother helps the docking process and increases the system's tolerance to pose uncertainties by mechanically aligning the mating parts in the final docking phase. A preliminary version of the algorithm was developed and field-tested on the Axel rover in the JPL Mars Yard. The algorithm achieved an 80% success rate in 40 experiments in both firm and loose soils and starting from up to 6 m away at up to 40 deg radial angle and 20 deg relative heading. The algorithm does not rely on an initial estimate of the relative pose. The preliminary results are promising and help retire the risk associated with the autonomous docking process enabling consideration in future martian and lunar missions.

Ensemble-based docking: From hit discovery to metabolism and toxicity predictions

DOE PAGES

Evangelista, Wilfredo; Weir, Rebecca; Ellingson, Sally; ...

2016-07-29

The use of ensemble-based docking for the exploration of biochemical pathways and toxicity prediction of drug candidates is described. We describe the computational engineering work necessary to enable large ensemble docking campaigns on supercomputers. We show examples where ensemble-based docking has significantly increased the number and the diversity of validated drug candidates. Finally, we illustrate how ensemble-based docking can be extended beyond hit discovery and toward providing a structural basis for the prediction of metabolism and off-target binding relevant to pre-clinical and clinical trials.

An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design.

PubMed

Ballante, Flavio; Marshall, Garland R

2016-01-25

Molecular docking is a widely used technique in drug design to predict the binding pose of a candidate compound in a defined therapeutic target. Numerous docking protocols are available, each characterized by different search methods and scoring functions, thus providing variable predictive capability on a same ligand-protein system. To validate a docking protocol, it is necessary to determine a priori the ability to reproduce the experimental binding pose (i.e., by determining the docking accuracy (DA)) in order to select the most appropriate docking procedure and thus estimate the rate of success in docking novel compounds. As common docking programs use generally different root-mean-square deviation (RMSD) formulas, scoring functions, and format results, it is both difficult and time-consuming to consistently determine and compare their predictive capabilities in order to identify the best protocol to use for the target of interest and to extrapolate the binding poses (i.e., best-docked (BD), best-cluster (BC), and best-fit (BF) poses) when applying a given docking program over thousands/millions of molecules during virtual screening. To reduce this difficulty, two new procedures called Clusterizer and DockAccessor have been developed and implemented for use with some common and "free-for-academics" programs such as AutoDock4, AutoDock4(Zn), AutoDock Vina, DOCK, MpSDockZn, PLANTS, and Surflex-Dock to automatically extrapolate BD, BC, and BF poses as well as to perform consistent cluster and DA analyses. Clusterizer and DockAccessor (code available over the Internet) represent two novel tools to collect computationally determined poses and detect the most predictive docking approach. Herein an application to human lysine deacetylase (hKDAC) inhibitors is illustrated.

Multiple receptor conformation docking, dock pose clustering and 3D QSAR studies on human poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors.

PubMed

Fatima, Sabiha; Jatavath, Mohan Babu; Bathini, Raju; Sivan, Sree Kanth; Manga, Vijjulatha

2014-10-01

Poly(ADP-ribose) polymerase-1 (PARP-1) functions as a DNA damage sensor and signaling molecule. It plays a vital role in the repair of DNA strand breaks induced by radiation and chemotherapeutic drugs; inhibitors of this enzyme have the potential to improve cancer chemotherapy or radiotherapy. Three-dimensional quantitative structure activity relationship (3D QSAR) models were developed using comparative molecular field analysis, comparative molecular similarity indices analysis and docking studies. A set of 88 molecules were docked into the active site of six X-ray crystal structures of poly(ADP-ribose)polymerase-1 (PARP-1), by a procedure called multiple receptor conformation docking (MRCD), in order to improve the 3D QSAR models through the analysis of binding conformations. The docked poses were clustered to obtain the best receptor binding conformation. These dock poses from clustering were used for 3D QSAR analysis. Based on MRCD and QSAR information, some key features have been identified that explain the observed variance in the activity. Two receptor-based QSAR models were generated; these models showed good internal and external statistical reliability that is evident from the [Formula: see text], [Formula: see text] and [Formula: see text]. The identified key features enabled us to design new PARP-1 inhibitors.

ATV docking ops

NASA Image and Video Library

2014-08-12

ISS040-E-091673 (12 Aug. 2014) --- In the Zvezda Service Module, European Space Agency astronaut Alexander Gerst (right) and Russian cosmonaut Alexander Skvortsov, both Expedition 40 flight engineers, take a brief moment for a photo during the approach and docking operations of ESA's "Georges Lemaitre" Automated Transfer Vehicle-5 (ATV-5) to the International Space Station.

33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles per hour. (b) In Huron Harbor, no vessel greater than 40 feet in length may exceed 6 miles per hour, except in the outer harbor where no vessel greater than 40 feet in length may exceed 10 miles per hour. Note...

33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles per hour. (b) In Huron Harbor, no vessel greater than 40 feet in length may exceed 6 miles per hour, except in the outer harbor where no vessel greater than 40 feet in length may exceed 10 miles per hour. Note...

33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles per hour. (b) In Huron Harbor, no vessel greater than 40 feet in length may exceed 6 miles per hour, except in the outer harbor where no vessel greater than 40 feet in length may exceed 10 miles per hour. Note...

33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles per hour. (b) In Huron Harbor, no vessel greater than 40 feet in length may exceed 6 miles per hour, except in the outer harbor where no vessel greater than 40 feet in length may exceed 10 miles per hour. Note...

33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles per hour. (b) In Huron Harbor, no vessel greater than 40 feet in length may exceed 6 miles per hour, except in the outer harbor where no vessel greater than 40 feet in length may exceed 10 miles per hour. Note...

Extracellular domains play different roles in gap junction formation and docking compatibility.

PubMed

Bai, Donglin; Wang, Ao Hong

2014-02-15

GJ (gap junction) channels mediate direct intercellular communication and play an important role in many physiological processes. Six connexins oligomerize to form a hemichannel and two hemichannels dock together end-to-end to form a GJ channel. Connexin extracellular domains (E1 and E2) have been shown to be important for the docking, but the molecular mechanisms behind the docking and formation of GJ channels are not clear. Recent developments in atomic GJ structure and functional studies on a series of connexin mutants revealed that E1 and E2 are likely to play different roles in the docking. Non-covalent interactions at the docking interface, including hydrogen bonds, are predicted to form between interdocked extracellular domains. Protein sequence alignment analysis on the docking compatible/incompatible connexins indicate that the E1 domain is important for the formation of the GJ channel and the E2 domain is important in the docking compatibility in heterotypic channels. Interestingly, the hydrogen-bond forming or equivalent residues in both E1 and E2 domains are mutational hot spots for connexin-linked human diseases. Understanding the molecular mechanisms of GJ docking can assist us to develop novel strategies in rescuing the disease-linked connexin mutants.

Fast and accurate grid representations for atom-based docking with partner flexibility.

PubMed

de Vries, Sjoerd J; Zacharias, Martin

2017-06-30

Macromolecular docking methods can broadly be divided into geometric and atom-based methods. Geometric methods use fast algorithms that operate on simplified, grid-like molecular representations, while atom-based methods are more realistic and flexible, but far less efficient. Here, a hybrid approach of grid-based and atom-based docking is presented, combining precalculated grid potentials with neighbor lists for fast and accurate calculation of atom-based intermolecular energies and forces. The grid representation is compatible with simultaneous multibody docking and can tolerate considerable protein flexibility. When implemented in our docking method ATTRACT, grid-based docking was found to be ∼35x faster. With the OPLSX forcefield instead of the ATTRACT coarse-grained forcefield, the average speed improvement was >100x. Grid-based representations may allow atom-based docking methods to explore large conformational spaces with many degrees of freedom, such as multiple macromolecules including flexibility. This increases the domain of biological problems to which docking methods can be applied. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

33 CFR 117.811 - Tonawanda Harbor.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Tonawanda Harbor. 117.811 Section 117.811 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements New York § 117.811 Tonawanda Harbor. The draw of the...

Pak functions downstream of Dock to regulate photoreceptor axon guidance in Drosophila.

PubMed

Hing, H; Xiao, J; Harden, N; Lim, L; Zipursky, S L

1999-06-25

The SH2/SH3 adaptor protein Dock has been proposed to transduce signals from guidance receptors to the actin cytoskeleton in Drosophila photoreceptor (R cell) growth cones. Here, we demonstrate that Drosophila p21-activated kinase (Pak) is required in a Dock pathway regulating R cell axon guidance and targeting. Dock and Pak colocalize to R cell axons and growth cones, physically interact, and their loss-of-function phenotypes are indistinguishable. Normal patterns of R cell connectivity require Pak's kinase activity and binding sites for both Dock and Cdc42/Rac. A membrane-tethered form of Pak (Pak(myr) acts as a dominant gain-of-function protein. Retinal expression of Pak(myr) rescues the R cell connectivity phenotype in dock mutants. These data establish Pak as a critical regulator of axon guidance and a downstream effector of Dock in vivo.

Tyurin packs the docking probe in Node 1 during Expedition Three

NASA Image and Video Library

2001-09-17

ISS003-E-5632 (17 September 2001) --- Cosmonaut Mikhail Tyurin, Expedition Three flight engineer, packs the docking probe in a stowage bag in Unity. Cosmonaut Vladimir Dezhurov, flight engineer, videotapes the event. The docking probe successfully guided the arrival of the Russian-built Pirs docking compartment to the International Space Station (ISS). Tyurin and Dezhurov represent Rosaviakosmos.

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

NASA Astrophysics Data System (ADS)

Lam, Polo C.-H.; Abagyan, Ruben; Totrov, Maxim

2018-01-01

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.

Companies hone in on radar-docking technology

NASA Astrophysics Data System (ADS)

Howell, Elizabeth

2009-11-01

As NASA prepares to retire the Space Shuttle next year, two private space firms have tested docking technology that could be used on the next generation of US spacecraft. In September, Canadian firm Neptec tested a new radar system on the Space Shuttle Discovery that allows spacecraft to dock more easily. Meanwhile, Space Exploration Technologies (SpaceX) based in California has revealed that it tested out a new proximity sensor, dubbed "Dragoneye", on an earlier shuttle mission in July.

Astronaut Richard Truly seen working with Apollo docking mechanism model

NASA Technical Reports Server (NTRS)

1975-01-01

Astronaut Richard H. Truly, an Apollo Soyuz Test Project (ASTP) spacecraft communicator, is seen working with an Apollo docking mechanism in the Mission Control Center during the joint U.S.-USSR ASTP docking in Earth orbit mission. Astronaut Truly, a member of the American ASTP crew support team, was working on the docking probe problem. The crew had notified ground control that there was a problem with removing the probe from the tunnel of the Apollo Command Module.

Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding.

PubMed

Pons, Carles; Solernou, Albert; Perez-Cano, Laura; Grosdidier, Solène; Fernandez-Recio, Juan

2010-11-15

We describe here our results in the last CAPRI edition. We have participated in all targets, both as predictors and as scorers, using our pyDock docking methodology. The new challenges (homology-based modeling of the interacting subunits, domain-domain assembling, and protein-RNA interactions) have pushed our computer tools to the limits and have encouraged us to devise new docking approaches. Overall, the results have been quite successful, in line with previous editions, especially considering the high difficulty of some of the targets. Our docking approaches succeeded in five targets as predictors or as scorers (T29, T34, T35, T41, and T42). Moreover, with the inclusion of available information on the residues expected to be involved in the interaction, our protocol would have also succeeded in two additional cases (T32 and T40). In the remaining targets (except T37), results were equally poor for most of the groups. We submitted the best model (in ligand RMSD) among scorers for the unbound-bound target T29, the second best model among scorers for the protein-RNA target T34, and the only correct model among predictors for the domain assembly target T35. In summary, our excellent results for the new proposed challenges in this CAPRI edition showed the limitations and applicability of our approaches and encouraged us to continue developing methodologies for automated biomolecular docking. © 2010 Wiley-Liss, Inc.

33 CFR 80.1136 - Moss Landing Harbor, CA.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Moss Landing Harbor, CA. 80.1136... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1136 Moss Landing Harbor, CA. A line drawn from the seaward extremity of the pier located 0.3 mile south of Moss Landing Harbor Entrance to the...

33 CFR 80.1136 - Moss Landing Harbor, CA.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Moss Landing Harbor, CA. 80.1136... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1136 Moss Landing Harbor, CA. A line drawn from the seaward extremity of the pier located 0.3 mile south of Moss Landing Harbor Entrance to the...

Docking and scoring protein interactions: CAPRI 2009.

PubMed

Lensink, Marc F; Wodak, Shoshana J

2010-11-15

Protein docking algorithms are assessed by evaluating blind predictions performed during 2007-2009 in Rounds 13-19 of the community-wide experiment on critical assessment of predicted interactions (CAPRI). We evaluated the ability of these algorithms to sample docking poses and to single out specific association modes in 14 targets, representing 11 distinct protein complexes. These complexes play important biological roles in RNA maturation, G-protein signal processing, and enzyme inhibition and function. One target involved protein-RNA interactions not previously considered in CAPRI, several others were hetero-oligomers, or featured multiple interfaces between the same protein pair. For most targets, predictions started from the experimentally determined structures of the free (unbound) components, or from models built from known structures of related or similar proteins. To succeed they therefore needed to account for conformational changes and model inaccuracies. In total, 64 groups and 12 web-servers submitted docking predictions of which 4420 were evaluated. Overall our assessment reveals that 67% of the groups, more than ever before, produced acceptable models or better for at least one target, with many groups submitting multiple high- and medium-accuracy models for two to six targets. Forty-one groups including four web-servers participated in the scoring experiment with 1296 evaluated models. Scoring predictions also show signs of progress evidenced from the large proportion of correct models submitted. But singling out the best models remains a challenge, which also adversely affects the ability to correctly rank docking models. With the increased interest in translating abstract protein interaction networks into realistic models of protein assemblies, the growing CAPRI community is actively developing more efficient and reliable docking and scoring methods for everyone to use. © 2010 Wiley-Liss, Inc.

DOVIS: an implementation for high-throughput virtual screening using AutoDock.

PubMed

Zhang, Shuxing; Kumar, Kamal; Jiang, Xiaohui; Wallqvist, Anders; Reifman, Jaques

2008-02-27

Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial. We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried. DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.

Expedition 27 Docking

NASA Image and Video Library

2011-04-06

View from the balcony of the Russian Mission Control Center in Korolev, Russia as the Soyuz TMA-21 nears the International Space Station on Thursday, April 7, 2011. The Soyuz TMA-21 docked to the International Space Station carrying Expedition 27 Soyuz Commander Alexander Samokutyaev, NASA Flight Engineer Ron Garan and Russian Flight Engineer Andrey Borisenko. Photo Credit: (NASA/Carla Cioffi)

Expedition 23 Docking

NASA Image and Video Library

2010-04-03

George Dyson, right, speaks to his wife NASA Flight Engineer Tracy Caldwell Dyson onboard the International Space Station from the Russian Mission Control Center, Korolev, Russia, Sunday, April 4, 2010. The Soyuz TMA-18 docked to the International Space Station carrying Expedition 23 Soyuz Commander Alexander Skvortsov, Flight Engineer Mikhail Kornienko and NASA Flight Engineer Tracy Caldwell Dyson. Photo Credit: (NASA/Carla Cioffi)

Expedition 25 Docking

NASA Image and Video Library

2010-10-09

The Soyuz TMA-01M nears its docking with the International Space Station as seen in the video monitor at Russian Mission Control Center in Korolev, Russia on Sunday, Oct. 10, 2010. The TMA-01M delivered the crew of Expedition 25 Soyuz Commander Alexander Kaleri, Flight Engineer Scott Kelly and Flight Engineer Oleg Skripochka to the ISS. Photo Credit: (NASA/Carla Cioffi)

77 FR 59551 - Safety Zone, Changes to Original Rule; Boston Harbor's Rock Removal Project, Boston Inner Harbor...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-28

... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket No. USCG-2012-0767] RIN 1625-AA00 Safety Zone, Changes to Original Rule; Boston Harbor's Rock Removal Project, Boston Inner Harbor... original provisions of that temporary final rule, but adds two additional safety zones necessary for the...

Space station full-scale docking/berthing mechanisms development

NASA Technical Reports Server (NTRS)

Burns, Gene C.; Price, Harold A.; Buchanan, David B.

1988-01-01

One of the most critical operational functions for the space station is the orbital docking between the station and the STS orbiter. The program to design, fabricate, and test docking/berthing mechanisms for the space station is described. The design reflects space station overall requirements and consists of two mating docking mechanism halves. One half is designed for use on the shuttle orbiter and incorporates capture and energy attenuation systems using computer controlled electromechanical actuators and/or attenuators. The mating half incorporates a flexible feature to allow two degrees of freedom at the module-to-module interface of the space station pressurized habitat volumes. The design concepts developed for the prototype units may be used for the first space station flight hardware.

Teaching about Pearl Harbor. Curriculum Enhancement Series #1.

ERIC Educational Resources Information Center

Shields, Anna Marshall

These materials consist of sample lesson plans for teaching about the Japanese attack on Pearl Harbor on December 7, 1941, in both U.S. and world history classes. The lesson plans challenge students to examine how current attitudes toward the Japanese may be rooted in World War II and Pearl Harbor. Selected bibliographies on Pearl Harbor, World…

Operator learning effects in teleoperated rendezvous & docking

NASA Astrophysics Data System (ADS)

Wilde, M.; Harder, J.; Purschke, R.

Teleoperation of spacecraft proximity operations and docking requires delicate timing and coordination of spacecraft maneuvers. Experience has shown that human operators show large performance fluctuations in these areas, which are a major factor to be addressed in operator training. In order to allow the quantification of the impact of these human fluctuations on control system performance and the human perception of this performance, a learning curve study was conducted with teleoperated final approach and docking scenarios. Over a period of ten experiment days, three test participants were tasked with repeatedly completing a set of three training scenarios. The scenarios were designed to contain different combinations of the major elements of any final approach and docking situation, and to feature an increasing difficulty level. The individual difficulty levels for the three operators furthermore differed in the level of operator support functions available in their human-machine interfaces. Operator performance in the test scenarios were evaluated in the fields approach success and precision, docking safety, and approach efficiency by a combination of recorded maneuver data and questionnaires. The results show that operator experience and the associated learning curves increase operator performance substantially, regardless of the support system used. The paper also shows that the fluctuations in operator performance and self-perception are substantial between as well as within experiment days, and must be reckoned with in teleoperation system design and mission planning.

2. Substructure of the main dock, looking south beneath the ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. Substructure of the main dock, looking south beneath the Hay and Grain Warehouse. Original log pilings have been encased in concrete. - Curtis Wharf, Main Dock, O & Second Streets, Anacortes, Skagit County, WA

2. General oblique view of north loading dock showing loading ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. General oblique view of north loading dock showing loading docks with doors opening into refrigerated rooms - Fort Hood, World War II Temporary Buildings, Cold Storage Building, Seventeenth Street, Killeen, Bell County, TX

JADOPPT: java based AutoDock preparing and processing tool.

PubMed

García-Pérez, Carlos; Peláez, Rafael; Therón, Roberto; Luis López-Pérez, José

2017-02-15

AutoDock is a very popular software package for docking and virtual screening. However, currently it is hard work to visualize more than one result from the virtual screening at a time. To overcome this limitation we have designed JADOPPT, a tool for automatically preparing and processing multiple ligand-protein docked poses obtained from AutoDock. It allows the simultaneous visual assessment and comparison of multiple poses through clustering methods. Moreover, it permits the representation of reference ligands with known binding modes, binding site residues, highly scoring regions for the ligand, and the calculated binding energy of the best ranked results. JADOPPT, supplementary material (Case Studies 1 and 2) and video tutorials are available at http://visualanalytics.land/cgarcia/JADOPPT.html. carlosgarcia@usal.es or pelaez@usal.es. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Dissecting Nck/Dock signaling pathways in Drosophila visual system.

PubMed

Rao, Yong

2005-01-01

The establishment of neuronal connections during embryonic development requires the precise guidance and targeting of the neuronal growth cone, an expanded cellular structure at the leading tip of a growing axon. The growth cone contains sophisticated signaling systems that allow the rapid communication between guidance receptors and the actin cytoskeleton in generating directed motility. Previous studies demonstrated a specific role for the Nck/Dock SH2/SH3 adapter protein in photoreceptor (R cell) axon guidance and target recognition in the Drosophila visual system, suggesting strongly that Nck/Dock is one of the long-sought missing links between cell surface receptors and the actin cytoskeleton. In this review, I discuss the recent progress on dissecting the Nck/Dock signaling pathways in R-cell growth cones. These studies have identified additional key components of the Nck/Dock signaling pathways for linking the receptor signaling to the remodeling of the actin cytoskeleton in controlling growth-cone motility.

Dissecting Nck/Dock Signaling Pathways in Drosophila Visual System

PubMed Central

2005-01-01

The establishment of neuronal connections during embryonic development requires the precise guidance and targeting of the neuronal growth cone, an expanded cellular structure at the leading tip of a growing axon. The growth cone contains sophisticated signaling systems that allow the rapid communication between guidance receptors and the actin cytoskeleton in generating directed motility. Previous studies demonstrated a specific role for the Nck/Dock SH2/SH3 adapter protein in photoreceptor (R cell) axon guidance and target recognition in the Drosophila visual system, suggesting strongly that Nck/Dock is one of the long-sought missing links between cell surface receptors and the actin cytoskeleton. In this review, I discuss the recent progress on dissecting the Nck/Dock signaling pathways in R-cell growth cones. These studies have identified additional key components of the Nck/Dock signaling pathways for linking the receptor signaling to the remodeling of the actin cytoskeleton in controlling growth-cone motility. PMID:15951852

Astronaut Vance Brand practices operating Docking Module hatch for ASTP

NASA Technical Reports Server (NTRS)

1975-01-01

Astronaut Vance D. Brand, command module pilot of the American Apollo Soyuz Test Project (ASTP) prime crew, practices operating a Docking Module hatch during ASTP pre-flight training at JSC. The Docking Module is designed to link the Apollo and Soyuz spacecraft during their docking in Earth orbit mission. Gary L. Doerre of JSC's Crew Training and Procedures Division is working with Brand. Doerre is wearing a face mask to help prevent possible exposure to Brand of disease prior to the ASTP launch.

A cross docking pipeline for improving pose prediction and virtual screening performance

NASA Astrophysics Data System (ADS)

Kumar, Ashutosh; Zhang, Kam Y. J.

2018-01-01

Pose prediction and virtual screening performance of a molecular docking method depend on the choice of protein structures used for docking. Multiple structures for a target protein are often used to take into account the receptor flexibility and problems associated with a single receptor structure. However, the use of multiple receptor structures is computationally expensive when docking a large library of small molecules. Here, we propose a new cross-docking pipeline suitable to dock a large library of molecules while taking advantage of multiple target protein structures. Our method involves the selection of a suitable receptor for each ligand in a screening library utilizing ligand 3D shape similarity with crystallographic ligands. We have prospectively evaluated our method in D3R Grand Challenge 2 and demonstrated that our cross-docking pipeline can achieve similar or better performance than using either single or multiple-receptor structures. Moreover, our method displayed not only decent pose prediction performance but also better virtual screening performance over several other methods.

The connection characteristics of flux pinned docking interface

NASA Astrophysics Data System (ADS)

Zhang, Mingliang; Han, Yanjun; Guo, Xing; Zhao, Cunbao; Deng, Feiyue

2017-03-01

This paper presents the mechanism and potential advantages of flux pinned docking interface mainly composed of a high temperature superconductor and an electromagnet. In order to readily assess the connection characteristics of flux pinned docking interface, the force between a high temperature superconductor and an electromagnet needs to be investigated. Based on the magnetic dipole method and the Ampere law method, the force between two current coils can be compared, which shows that the Ampere law method has the higher calculated accuracy. Based on the improved frozen image model and the Ampere law method, the force between high temperature superconductor bulk and permanent magnet can be calculated, which is validated experimentally. Moreover, the force between high temperature superconductor and electromagnet applied to flux pinned docking interface is able to be predicted and analyzed. The connection stiffness between high temperature superconductor and permanent magnet can be calculated based on the improved frozen image model and Hooke's law. The relationship between the connection stiffness and field cooling height is analyzed. Furthermore, the connection stiffness of the flux pinned docking interface is predicted and optimized, and its effective working range is defined and analyzed in case of some different parameters.

20. VIEW OF EAST END OF SPERRY OCEAN DOCK, SHOWING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

20. VIEW OF EAST END OF SPERRY OCEAN DOCK, SHOWING SOUTH AND EAST ELEVATION, INCLUDING PORTION OF THE SPERRY OCEAN DOCK DECK, LOOKING NORTH - Puget Sound Flouring Mills, 611 Schuster Parkway, Tacoma, Pierce County, WA

Artist's concept of Apollo/Soyuz spacecraft docking approach

NASA Image and Video Library

1973-08-01

S73-02395 (August 1973) --- An artist?s concept illustrating an Apollo-type spacecraft (on left) about to dock with a Soviet Soyuz-type spacecraft. A recent agreement between the United States and the Union of Soviet Socialist Republics provides for the docking in space of the Soyuz and Apollo-type spacecraft in Earth orbit in 1975. The joint venture is called the Apollo-Soyuz Test Project.

Quantification of total mercury in liver and heart tissue of Harbor Seals (Phoca vitulina) from Alaska USA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marino, Kady B.; Hoover-Miller, Anne; Conlon, Suzanne

This study quantified the Hg levels in the liver (n=98) and heart (n=43) tissues of Harbor Seals (Phoca vitulina) (n=102) harvested from Prince William Sound and Kodiak Island Alaska. Mercury tissue dry weight (dw) concentrations in the liver ranged from 1.7 to 393 ppm dw, and in the heart from 0.19 to 4.99 ppm dw. Results of this study indicate liver and heart tissues' Hg ppm dw concentrations significantly increase with age. Male Harbor Seals bioaccumulated Hg in both their liver and heart tissues at a significantly faster rate than females. The liver Hg bioaccumulation rates between the harvest locationsmore » Kodiak Island and Prince William Sound were not found to be significantly different. On adsorption Hg is transported throughout the Harbor Seal's body with the partition coefficient higher for the liver than the heart. No significant differences in the bio-distribution (liver:heart Hg ppm dw ratios (n=38)) values were found with respect to either age, sex or geographic harvest location. In this study the age at which Hg liver and heart bioaccumulation levels become significantly distinct in male and female Harbor Seals were identified through a Tukey's analysis. Of notably concern to human health was a male Harbor Seal's liver tissue harvested from Kodiak Island region. Mercury accumulation in this sample tissue was determined through a Q-test to be an outlier, having far higher Hg concentrarion (liver 392 Hg ppm dw) than the general population sampled. - Highlights: Black-Right-Pointing-Pointer Mercury accumulation in the liver and heart of seals exceed food safety guidelines. Black-Right-Pointing-Pointer Accumulation rate is greater in males than females with age. Black-Right-Pointing-Pointer Liver mercury accumulation is greater than in the heart tissues. Black-Right-Pointing-Pointer Mercury determination by USA EPA Method 7473 using thermal decomposition.« less

NASA Docking System (NDS) Interface Definitions Document (IDD). Revision F, Dec. 15, 2011

NASA Technical Reports Server (NTRS)

Lewis, James

2011-01-01

The NASA Docking System (NDS) mating system supports low approach velocity docking and provides a modular and reconfigurable standard interface, supporting crewed and autonomous vehicles during mating and assembly operations. The NDS is NASA s implementation for the International Docking System Standard (IDSS) using low impact docking technology. All NDS configurations can mate with the configuration specified in the IDSS Interface Definition Document (IDD), Revision A, released May 13, 2011. The NDS evolved from the Low Impact Docking System (LIDS). The term (and its associated acronym), international Low Impact Docking System (iLIDS) is also used to describe this system. NDS and iLIDS may be used interchangeability. Some of the heritage documentation and implementations (e.g., software command names) used on the NDS will continue to use the LIDS acronym.

Expedition 27 Docking

NASA Image and Video Library

2011-04-06

The Soyuz TMA-21 is seen as it approaches the International Space Station on a large screen TV at the Russian Mission Control Center in Korolev, Russia on Thursday, April 7, 2011. The Soyuz TMA-21 docked to the International Space Station carrying Expedition 27 Soyuz Commander Alexander Samokutyaev, NASA Flight Engineer Ron Garan and Russian Flight Engineer Andrey Borisenko. Photo Credit: (NASA/Carla Cioffi)

Expedition 23 Docking

NASA Image and Video Library

2010-04-03

A large TV screen in Russian Mission Control Center in Korolev, Russia shows Expedition 23 Commander Oleg Kotov, right, welcoming NASA astronaut and Flight Engineer Tracy Caldwell Dyson onboard the International Space Station after she and fellow crew members Expedition 23 Soyuz Commander Alexander Skvortsov and Flight Engineer Mikhail Kornienko docked their Soyuz TMA-18 spacecraft on Sunday, April 4, 2010. Photo Credit: (NASA/Carla Cioffi)

Expedition 23 Docking

NASA Image and Video Library

2010-04-03

Mary Ellen Caldwell, center, speaks to her daughter NASA Flight Engineer Tracy Caldwell Dyson onboard the International Space Station from the Russian Mission Control Center, Korolev, Russia, Sunday, April 4, 2010. The Soyuz TMA-18 docked to the International Space Station carrying Expedition 23 Soyuz Commander Alexander Skvortsov, Flight Engineer Mikhail Kornienko and NASA Flight Engineer Tracy Caldwell Dyson. Photo Credit: (NASA/Carla Cioffi)

Leucothoe eltoni sp. n., a new species of commensal leucothoid amphipod from coral reefs in Raja Ampat, Indonesia (Crustacea, Amphipoda).

PubMed

Thomas, James Darwin

2015-01-01

A new species of leucothoid amphipod, Leucothoe eltoni sp. n., is described from coral reefs in Raja Ampat, Indonesia where it inhabits the branchial chambers of solitary tunicates. With an inflated first gnathopod superficially resembling the genus Paraleucothoe, this new species has a two-articulate maxilla 1 palp characteristic of the genus Leucothoe. While described from coral reef environments in tropical Indonesia and the Philippines, it is an established invasive species in the Hawaiian Islands. The most likely mode of introduction was a US Navy dry dock transported to Pearl Harbor in 1992 from Subic Bay, Philippines.

Astronaut Brand and Cosmonaut Ivanchenko in Docking Module trainer

NASA Technical Reports Server (NTRS)

1974-01-01

Astronaut Vance D. Brand (foreground) and Cosmonaut Aleksandr S. Ivanchenko are seated in the Docking Module trainer in bldg 35 during Apollo Soyuz Test Project (ASTP) simulation training at JSC. Brand is the command module pilot of the American ASTP prime crew. Ivanchenko is the engineer on the Soviet ASTP fourth crew (back-up). During the exercise the American ASTP crew and the Soviet ASTP crew simulated docking the Apollo and Soyuz in Earth orbit and transferring to each other's spacecraft. This view is looking from inside the Command Module into the Docking Module. The hatchway leading into the Soyuz spacecraft orbital module mock-up is in the background.

One Year Crew Docking to the International Space Station

NASA Image and Video Library

2015-05-27

This video was taken by the crew members aboard the Soyuz TMA-16M spacecraft which docked to the International Space Station at 9:33 p.m. EDT March 27, 2015. NASA astronaut Scott Kelly and Russian cosmonauts Mikhail Kornienko and Gennady Padalka arrived just six hours after launching from Baikonur, Kazakhstan, completing four orbits around the Earth before catching up with the orbiting laboratory. The vehicle docked to the Poisk module (also known as the Mini-Research Module 2) on the space-facing side of the Russian Service Module. The spinning object in view is an antenna that is part of the automatic rendezvous and docking system known as KURS.

Space Shuttle Program (SSP) Dual Docked Operations (DDO)

NASA Technical Reports Server (NTRS)

Sills, Joel W., Jr.; Bruno, Erica E.

2016-01-01

This document describes the concept definition, studies, and analysis results generated by the Space Shuttle Program (SSP), International Space Station (ISS) Program (ISSP), and Mission Operations Directorate for implementing Dual Docked Operations (DDO) during mated Orbiter/ISS missions. This work was performed over a number of years. Due to the ever increasing visiting vehicle traffic to and from the ISS, it became apparent to both the ISSP and the SSP that there would arise occasions where conflicts between a visiting vehicle docking and/or undocking could overlap with a planned Space Shuttle launch and/or during docked operations. This potential conflict provided the genesis for evaluating risk mitigations to gain maximum flexibility for managing potential visiting vehicle traffic to and from the ISS and to maximize launch and landing opportunities for all visiting vehicles.

4. South (shore) end of dock as viewed from shore ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. South (shore) end of dock as viewed from shore looking north includes section of creosote pipe as it leaves the shore. - Pacific Creosoting Plant, Oil-Creosote Unloading Dock, 5350 Creosote Place, Northeast, Bremerton, Kitsap County, WA

[Pearl Harbor.

ERIC Educational Resources Information Center

Johnson, Jennifer, Ed.

1992-01-01

This issue of "Loblolly Magazine" was written in observance of the 50th anniversary of the U.S. entrance into World War II. The publication features interviews conducted by East Texas high school students with Clarence Otterman, one of the few survivors of the crew of the USS Arizona, which was bombed during the attack on Pearl Harbor,…

Machine learning in computational docking.

PubMed

Khamis, Mohamed A; Gomaa, Walid; Ahmed, Walaa F

2015-03-01

The objective of this paper is to highlight the state-of-the-art machine learning (ML) techniques in computational docking. The use of smart computational methods in the life cycle of drug design is relatively a recent development that has gained much popularity and interest over the last few years. Central to this methodology is the notion of computational docking which is the process of predicting the best pose (orientation + conformation) of a small molecule (drug candidate) when bound to a target larger receptor molecule (protein) in order to form a stable complex molecule. In computational docking, a large number of binding poses are evaluated and ranked using a scoring function. The scoring function is a mathematical predictive model that produces a score that represents the binding free energy, and hence the stability, of the resulting complex molecule. Generally, such a function should produce a set of plausible ligands ranked according to their binding stability along with their binding poses. In more practical terms, an effective scoring function should produce promising drug candidates which can then be synthesized and physically screened using high throughput screening process. Therefore, the key to computer-aided drug design is the design of an efficient highly accurate scoring function (using ML techniques). The methods presented in this paper are specifically based on ML techniques. Despite many traditional techniques have been proposed, the performance was generally poor. Only in the last few years started the application of the ML technology in the design of scoring functions; and the results have been very promising. The ML-based techniques are based on various molecular features extracted from the abundance of protein-ligand information in the public molecular databases, e.g., protein data bank bind (PDBbind). In this paper, we present this paradigm shift elaborating on the main constituent elements of the ML approach to molecular docking along

Docking of Natural Products against Neurodegenerative Diseases: General Concepts.

PubMed

Ribeiro, Frederico F; Mendonca Junior, Francisco J B; Ghasemi, Jahan B; Ishiki, Hamilton M; Scotti, Marcus T; Scotti, Luciana

2018-01-01

Since antiquity, humanity has used medicinal plant preparations to cure its ills, and, as research has progressed, new technologies have enabled more investigations on natural compounds which originate from plants, fungi, and marine species. The health benefits that these natural products provide have become a motive for treatment studies of various diseases. Among them, the neurodegenerative diseases like Alzheimer's and Parkinson's, a major age-related neurodegenerative disorder. Studies with natural products for neurodegenerative diseases (particularly through molecular docking) search for, and then focus on those ligands which offer effective inhibition of the enzymes monoamine oxidase and acetylcholinesterase. This review introduces the main concepts involved in docking studies with natural products: and also in our group, which has conducted a docking study of natural products isolated from Tetrapterys mucronata for inhibition of acetylcholinesterase. We observed that compounds 4 and 5 formed more interactions than the theoretical ligand, but that ligands with greater activity also interacted with residues HIS 381 and GLN 527. We have reported on our docking study performed with AChE and alkaloids isolated from the plant Tetrapterys mucronata. Our docking results corroborate the experiments conducted, and emphasize the positive contribution that these theoretical studies involving natural products bring to the fight against neurodegenerative diseases. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Molecular Docking and Drug Discovery in β-Adrenergic Receptors.

PubMed

Vilar, Santiago; Sobarzo-Sanchez, Eduardo; Santana, Lourdes; Uriarte, Eugenio

2017-01-01

Evolution in computer engineering, availability of increasing amounts of data and the development of new and fast docking algorithms and software have led to improved molecular simulations with crucial applications in virtual high-throughput screening and drug discovery. Moreover, analysis of protein-ligand recognition through molecular docking has become a valuable tool in drug design. In this review, we focus on the applicability of molecular docking on a particular class of G protein-coupled receptors: the β-adrenergic receptors, which are relevant targets in clinic for the treatment of asthma and cardiovascular diseases. We describe the binding site in β-adrenergic receptors to understand key factors in ligand recognition along with the proteins activation process. Moreover, we focus on the discovery of new lead compounds that bind the receptors, on the evaluation of virtual screening using the active/ inactive binding site states, and on the structural optimization of known families of binders to improve β-adrenergic affinity. We also discussed strengths and challenges related to the applicability of molecular docking in β-adrenergic receptors. Molecular docking is a valuable technique in computational chemistry to deeply analyze ligand recognition and has led to important breakthroughs in drug discovery and design in the field of β-adrenergic receptors. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

50 CFR 86.13 - What is boating infrastructure?

Code of Federal Regulations, 2010 CFR

2010-10-01

..., currents, etc., that provide a temporary safe anchorage point or harbor of refuge during storms); (f) Floating docks and fixed piers; (g) Floating and fixed breakwaters; (h) Dinghy docks (floating or fixed...

A primer on wood as dock construction material

Treesearch

Stan Lebow

2007-01-01

To be a successful marina owner and operator, it’s important to understand all the facets of one’s facility, including the intricacies of one part of the marina that most boaters take for granted: the docks. When it comes to dock construction, marinas have a wide-range of materials to choose from, with one of the most commonly used materials being preservative-treated...

Connection stiffness and dynamical docking process of flux pinned spacecraft modules

NASA Astrophysics Data System (ADS)

Lu, Yong; Zhang, Mingliang; Gao, Dong

2014-02-01

This paper describes a novel kind of potential flux pinned docking system that consists of guidance navigation and control system, the traditional extrusion type propulsion system, and a flux pinned docking interface. Because of characteristics of passive stability of flux pinning, the docking control strategy of flux pinned docking system only needs a series of sequential control rather than necessary active feedback control, as well as avoidance of hazardous collision accident. The flux pinned force between YBaCuO (YBCO) high temperature superconductor bulk and permanent magnet is able to be given vent based on the identical current loop model and improved image dipole model, which can be validated experimentally. Thus, the connection stiffness between two flux pinned spacecraft modules can be calculated based on Hooke's law. This connection stiffness matrix at the equilibrium position has the positive definite performance, which can validate the passively stable connection of two flux pinned spacecraft modules theoretically. Furthermore, the relative orbital dynamical equation of two flux pinned spacecraft modules can be established based on Clohessy-Wiltshire's equations and improved image dipole model. The dynamical docking process between two flux pinned spacecraft modules can be obtained by way of numerical simulation, which suggests the feasibility of flux pinned docking system.

Connection stiffness and dynamical docking process of flux pinned spacecraft modules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Yong; Zhang, Mingliang, E-mail: niudun12@126.com; Gao, Dong

2014-02-14

This paper describes a novel kind of potential flux pinned docking system that consists of guidance navigation and control system, the traditional extrusion type propulsion system, and a flux pinned docking interface. Because of characteristics of passive stability of flux pinning, the docking control strategy of flux pinned docking system only needs a series of sequential control rather than necessary active feedback control, as well as avoidance of hazardous collision accident. The flux pinned force between YBaCuO (YBCO) high temperature superconductor bulk and permanent magnet is able to be given vent based on the identical current loop model and improvedmore » image dipole model, which can be validated experimentally. Thus, the connection stiffness between two flux pinned spacecraft modules can be calculated based on Hooke's law. This connection stiffness matrix at the equilibrium position has the positive definite performance, which can validate the passively stable connection of two flux pinned spacecraft modules theoretically. Furthermore, the relative orbital dynamical equation of two flux pinned spacecraft modules can be established based on Clohessy-Wiltshire's equations and improved image dipole model. The dynamical docking process between two flux pinned spacecraft modules can be obtained by way of numerical simulation, which suggests the feasibility of flux pinned docking system.« less

Expedition 54 Soyuz Docking

NASA Image and Video Library

2017-12-19

U.S. Ambassador to Russia Jon Huntsman Jr. is seen during an interview with NASA Public Affairs Office Rob Navias in the Moscow Mission Control Center in Korolev, Russia after the Soyuz MS-07 spacecraft docked with the International Space Station, Tuesday, Dec. 19, 2017. Photo Credit: (NASA/Joel Kowsky)

29. ORE DOCK, LOOKING WEST; AT WORK UNLOADING THE 'GEORGE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

29. ORE DOCK, LOOKING WEST; AT WORK UNLOADING THE 'GEORGE M. HUMPHREY'S' CARGO OF 25,000. TONS OF ORE. - Pennsylvania Railway Ore Dock, Lake Erie at Whiskey Island, approximately 1.5 miles west of Public Square, Cleveland, Cuyahoga County, OH

1. Dyea Dock looking south. Note faint evenly spaced circular ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. Dyea Dock looking south. Note faint evenly spaced circular dark pieces of grass up through the middle of the picture indicating posts making up the pier. Photograph made from park service cherry picker. - Dyea Dock & Association (Ruins), Skagway, Skagway, AK

Artist's concept of scene in Earth orbit during transposition and docking

NASA Technical Reports Server (NTRS)

1975-01-01

An artist's concept depicting a scene in Earth orbit during the Apollo transposition and docking maneuvers of the Apollo Soyuz Test Project (ASTP) mission. The Command/Service Module is moving into position to dock with the Docking Module. This scene will take place some one hour and twenty-three minutes after the Apollo-Saturn 1B liftoff from the Kennedy Space Center on July 15, 1975. The artwork is by Paul Fjeld.

I-AUV Docking and Panel Intervention at Sea

PubMed Central

Palomeras, Narcís; Peñalver, Antonio; Massot-Campos, Miquel; Negre, Pep Lluís; Fernández, José Javier; Ridao, Pere; Sanz, Pedro J.; Oliver-Codina, Gabriel

2016-01-01

The use of commercially available autonomous underwater vehicles (AUVs) has increased during the last fifteen years. While they are mainly used for routine survey missions, there is a set of applications that nowadays can be only addressed by manned submersibles or work-class remotely operated vehicles (ROVs) equipped with teleoperated arms: the intervention applications. To allow these heavy vehicles controlled by human operators to perform intervention tasks, underwater structures like observatory facilities, subsea panels or oil-well Christmas trees have been adapted, making them more robust and easier to operate. The TRITON Spanish founded project proposes the use of a light-weight intervention AUV (I-AUV) to carry out intervention applications simplifying the adaptation of these underwater structures and drastically reducing the operational cost. To prove this concept, the Girona 500 I-AUV is used to autonomously dock into an adapted subsea panel and once docked perform an intervention composed of turning a valve and plugging in/unplugging a connector. The techniques used for the autonomous docking and manipulation as well as the design of an adapted subsea panel with a funnel-based docking system are presented in this article together with the results achieved in a water tank and at sea. PMID:27754348

I-AUV Docking and Panel Intervention at Sea.

PubMed

Palomeras, Narcís; Peñalver, Antonio; Massot-Campos, Miquel; Negre, Pep Lluís; Fernández, José Javier; Ridao, Pere; Sanz, Pedro J; Oliver-Codina, Gabriel

2016-10-12

The use of commercially available autonomous underwater vehicles (AUVs) has increased during the last fifteen years. While they are mainly used for routine survey missions, there is a set of applications that nowadays can be only addressed by manned submersibles or work-class remotely operated vehicles (ROVs) equipped with teleoperated arms: the intervention applications. To allow these heavy vehicles controlled by human operators to perform intervention tasks, underwater structures like observatory facilities, subsea panels or oil-well Christmas trees have been adapted, making them more robust and easier to operate. The TRITON Spanish founded project proposes the use of a light-weight intervention AUV (I-AUV) to carry out intervention applications simplifying the adaptation of these underwater structures and drastically reducing the operational cost. To prove this concept, the Girona 500 I-AUV is used to autonomously dock into an adapted subsea panel and once docked perform an intervention composed of turning a valve and plugging in/unplugging a connector. The techniques used for the autonomous docking and manipulation as well as the design of an adapted subsea panel with a funnel-based docking system are presented in this article together with the results achieved in a water tank and at sea.

Launch of Agena Target Docking Vehicle atop Atlas launch vehicle

NASA Technical Reports Server (NTRS)

1966-01-01

An Agena Target Docking Vehicle atop its Atlas launch vehicle was launched fromt the Kennedy Space Center's Launch Complex 14 at 6:05 a.m., September 12, 1966. The Agena served as a rendezvous and docking vehicle for the Gemini 11 spacecraft.

Accessible high-throughput virtual screening molecular docking software for students and educators.

PubMed

Jacob, Reed B; Andersen, Tim; McDougal, Owen M

2012-05-01

We survey low cost high-throughput virtual screening (HTVS) computer programs for instructors who wish to demonstrate molecular docking in their courses. Since HTVS programs are a useful adjunct to the time consuming and expensive wet bench experiments necessary to discover new drug therapies, the topic of molecular docking is core to the instruction of biochemistry and molecular biology. The availability of HTVS programs coupled with decreasing costs and advances in computer hardware have made computational approaches to drug discovery possible at institutional and non-profit budgets. This paper focuses on HTVS programs with graphical user interfaces (GUIs) that use either DOCK or AutoDock for the prediction of DockoMatic, PyRx, DockingServer, and MOLA since their utility has been proven by the research community, they are free or affordable, and the programs operate on a range of computer platforms.

32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 5 2010-07-01 2010-07-01 false Regulations for Pearl Harbor, Hawaii. 765.6... RULES RULES APPLICABLE TO THE PUBLIC § 765.6 Regulations for Pearl Harbor, Hawaii. The Commander, U.S. Naval Base, Pearl Harbor, Hawaii, is responsible for prescribing and enforcing such rules and...

Rational Drug Discovery of HCV Helicase Inhibitor: Improved Docking Accuracy with Multiple Seeding in AutoDock Vina and In Situ Minimization.

PubMed

Lim, See K; Othman, Rozana; Yusof, Rohana; Heh, Choon H

2017-01-01

Hepatitis C is a significant cause for end-stage liver diseases and liver transplantation which affects approximately 3% of the global populations. Despite the current several direct antiviral agents in the treatment of Hepatitis C, the standard treatment for HCV infection is accompanied by several drawbacks, such as adverse side effects, high pricing of medications and the rapid emerging rate of resistant HCV variants. To discover potential inhibitors for HCV helicase through an optimized in silico approach. In this study, a homology model (HCV Genotype 3 helicase) was used as the target and screened through a benzopyran-based virtual library. Multiple-seedings of AutoDock Vina and in situ minimization were to account for the non-deterministic nature of AutoDock Vina search algorithm and binding site flexibility, respectively. ADME/T and interaction analyses were also done on the top hits via FAFDRUG3 web server and Discovery Studio 4.5. This study involved the development of an improved flow for virtual screening via implemention of multiple-seeding screening approach and in situ minimization. With the new docking protocol, the redocked standards have shown better RMSD value in reference to their native conformations. Ten benzopyran-like compounds with satisfactory physicochemical properties were discovered to be potential inhibitors of HCV helicase. ZINC38649350 was identified as the most potential inhibitor. Ten potential HCV helicase inhibitors were discovered via a new docking optimization protocol with better docking accuracy. These findings could contribute to the discovery of novel HCV antivirals and serve as an alternative approach of in silico rational drug discovery. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

NASA Docking System (NDS) Interface Definitions Document (IDD). Revision C, Nov. 2010

NASA Technical Reports Server (NTRS)

2010-01-01

The NASA Docking System (NDS) mating system supports low approach velocity docking and provides a modular and reconfigurable standard interface, supporting crewed and autonomous vehicles during mating and assembly operations. The NDS is NASA's implementation for the emerging International Docking System Standard (IDSS) using low impact docking technology. All NDS configurations can mate with the configuration specified in the IDSS Interface Definition Document (IDD) released September 21, 2010. The NDS evolved from the Low Impact Docking System (LIDS). The acronym international Low Impact Docking System (iLIDS) is also used to describe this system. NDS and iLIDS may be used interchangeability. Some of the heritage documentation and implementations (e.g., software command names) used on NDS will continue to use the LIDS acronym. The NDS IDD defines the interface characteristics and performance capability of the NDS, including uses ranging from crewed to autonomous space vehicles and from low earth orbit to deep space exploration. The responsibility for developing space vehicles and for making them technically and operationally compatible with the NDS rests with the vehicle providers. Host vehicle examples include crewed/uncrewed spacecraft, space station modules, elements, etc. Within this document, any docking space vehicle will be referred to as the host vehicle. This document defines the NDS-to-NDS interfaces, as well as the NDS-to-host vehicle interfaces and performance capability.

PtdIns(4,5)P2 is not required for secretory granule docking.

PubMed

Omar-Hmeadi, Muhmmad; Gandasi, Nikhil R; Barg, Sebastian

2018-06-01

Phosphoinositides (PtdIns) play important roles in exocytosis and are thought to regulate secretory granule docking by co-clustering with the SNARE protein syntaxin to form a docking receptor in the plasma membrane. Here we tested this idea by high-resolution total internal reflection imaging of EGFP-labeled PtdIns markers or syntaxin-1 at secretory granule release sites in live insulin-secreting cells. In intact cells, PtdIns markers distributed evenly across the plasma membrane with no preference for granule docking sites. In contrast, syntaxin-1 was found clustered in the plasma membrane, mostly beneath docked granules. We also observed rapid accumulation of syntaxin-1 at sites where granules arrived to dock. Acute depletion of plasma membrane phosphatidylinositol (4,5) bisphosphate (PtdIns(4,5)P 2 ) by recruitment of a 5'-phosphatase strongly inhibited Ca 2+ -dependent exocytosis, but had no effect on docked granules or the distribution and clustering of syntaxin-1. Cell permeabilization by α-toxin or formaldehyde-fixation caused PtdIns marker to slowly cluster, in part near docked granules. In summary, our data indicate that PtdIns(4,5)P 2 accelerates granule priming, but challenge a role of PtdIns in secretory granule docking or clustering of syntaxin-1 at the release site. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

iATTRACT: simultaneous global and local interface optimization for protein-protein docking refinement.

PubMed

Schindler, Christina E M; de Vries, Sjoerd J; Zacharias, Martin

2015-02-01

Protein-protein interactions are abundant in the cell but to date structural data for a large number of complexes is lacking. Computational docking methods can complement experiments by providing structural models of complexes based on structures of the individual partners. A major caveat for docking success is accounting for protein flexibility. Especially, interface residues undergo significant conformational changes upon binding. This limits the performance of docking methods that keep partner structures rigid or allow limited flexibility. A new docking refinement approach, iATTRACT, has been developed which combines simultaneous full interface flexibility and rigid body optimizations during docking energy minimization. It employs an atomistic molecular mechanics force field for intermolecular interface interactions and a structure-based force field for intramolecular contributions. The approach was systematically evaluated on a large protein-protein docking benchmark, starting from an enriched decoy set of rigidly docked protein-protein complexes deviating by up to 15 Å from the native structure at the interface. Large improvements in sampling and slight but significant improvements in scoring/discrimination of near native docking solutions were observed. Complexes with initial deviations at the interface of up to 5.5 Å were refined to significantly better agreement with the native structure. Improvements in the fraction of native contacts were especially favorable, yielding increases of up to 70%. © 2014 Wiley Periodicals, Inc.

Optimization of protein-protein docking for predicting Fc-protein interactions.

PubMed

Agostino, Mark; Mancera, Ricardo L; Ramsland, Paul A; Fernández-Recio, Juan

2016-11-01

The antibody crystallizable fragment (Fc) is recognized by effector proteins as part of the immune system. Pathogens produce proteins that bind Fc in order to subvert or evade the immune response. The structural characterization of the determinants of Fc-protein association is essential to improve our understanding of the immune system at the molecular level and to develop new therapeutic agents. Furthermore, Fc-binding peptides and proteins are frequently used to purify therapeutic antibodies. Although several structures of Fc-protein complexes are available, numerous others have not yet been determined. Protein-protein docking could be used to investigate Fc-protein complexes; however, improved approaches are necessary to efficiently model such cases. In this study, a docking-based structural bioinformatics approach is developed for predicting the structures of Fc-protein complexes. Based on the available set of X-ray structures of Fc-protein complexes, three regions of the Fc, loosely corresponding to three turns within the structure, were defined as containing the essential features for protein recognition and used as restraints to filter the initial docking search. Rescoring the filtered poses with an optimal scoring strategy provided a success rate of approximately 80% of the test cases examined within the top ranked 20 poses, compared to approximately 20% by the initial unrestrained docking. The developed docking protocol provides a significant improvement over the initial unrestrained docking and will be valuable for predicting the structures of currently undetermined Fc-protein complexes, as well as in the design of peptides and proteins that target Fc. Copyright © 2016 John Wiley & Sons, Ltd.

ASTP crewmen in Docking Module trainer during training session at JSC

NASA Technical Reports Server (NTRS)

1975-01-01

An interior view of the Docking Module trainer in bldg 35 during Apollo Soyuz Test Project (ASTP) joint crew training at JSC. Astronaut Donald K. Slayton (right) is the docking module pilot of the American ASTP prime crew. The other man is Cosmonaut Valeriy N. Kubasov, engineer on the Soviet ASTP first (prime) crew. The training session simulated activities on the second day in space. The Docking module is designed to link the Apollo and Soyuz spacecraft.

GPU acceleration of Dock6's Amber scoring computation.

PubMed

Yang, Hailong; Zhou, Qiongqiong; Li, Bo; Wang, Yongjian; Luan, Zhongzhi; Qian, Depei; Li, Hanlu

2010-01-01

Dressing the problem of virtual screening is a long-term goal in the drug discovery field, which if properly solved, can significantly shorten new drugs' R&D cycle. The scoring functionality that evaluates the fitness of the docking result is one of the major challenges in virtual screening. In general, scoring functionality in docking requires a large amount of floating-point calculations, which usually takes several weeks or even months to be finished. This time-consuming procedure is unacceptable, especially when highly fatal and infectious virus arises such as SARS and H1N1, which forces the scoring task to be done in a limited time. This paper presents how to leverage the computational power of GPU to accelerate Dock6's (http://dock.compbio.ucsf.edu/DOCK_6/) Amber (J. Comput. Chem. 25: 1157-1174, 2004) scoring with NVIDIA CUDA (NVIDIA Corporation Technical Staff, Compute Unified Device Architecture - Programming Guide, NVIDIA Corporation, 2008) (Compute Unified Device Architecture) platform. We also discuss many factors that will greatly influence the performance after porting the Amber scoring to GPU, including thread management, data transfer, and divergence hidden. Our experiments show that the GPU-accelerated Amber scoring achieves a 6.5× speedup with respect to the original version running on AMD dual-core CPU for the same problem size. This acceleration makes the Amber scoring more competitive and efficient for large-scale virtual screening problems.

Pilot in Rendezvous Docking Simulator

NASA Image and Video Library

1962-12-19

Unidentified Pilot eyeballs his way to a docking by peering through the portal in his capsule. Photo published in Spaceflight Revolution, NASA Langley Research Center From Sputnik to Apollo. By James R. Hansen. NASA SP-4308, 1995, p. 372.

22. Detail of interior corner showing truss system, dock no. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

22. Detail of interior corner showing truss system, dock no. 492. View to south. - Offutt Air Force Base, Looking Glass Airborne Command Post, Nose Docks, On either side of Hangar Access Apron at Northwest end of Project Looking Glass Historic District, Bellevue, Sarpy County, NE

22. ORE STORAGE BRIDGE AT PLANT'S LOWER DOCK, LOOKING SOUTH. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

22. ORE STORAGE BRIDGE AT PLANT'S LOWER DOCK, LOOKING SOUTH. THE WELLMAN ORE BRIDGE (THERE ARE TWO AT THIS DOCK) WERE ERECTED IN 1908 BY THE CORRIGAN, McKINNEY COMPANY. - Corrigan, McKinney Steel Company, 3100 East Forty-fifth Street, Cleveland, Cuyahoga County, OH

33 CFR 110.132 - Rockland Harbor, Maine.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Rockland Harbor, Maine. 110.132... ANCHORAGE REGULATIONS Anchorage Grounds § 110.132 Rockland Harbor, Maine. (a) The anchorage grounds—(1..., power plant, oil terminal, marine terminal, munitions plant, military or naval arsenal or depot...

33 CFR 110.132 - Rockland Harbor, Maine.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Rockland Harbor, Maine. 110.132... ANCHORAGE REGULATIONS Anchorage Grounds § 110.132 Rockland Harbor, Maine. (a) The anchorage grounds—(1..., power plant, oil terminal, marine terminal, munitions plant, military or naval arsenal or depot...

33 CFR 110.132 - Rockland Harbor, Maine.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Rockland Harbor, Maine. 110.132... ANCHORAGE REGULATIONS Anchorage Grounds § 110.132 Rockland Harbor, Maine. (a) The anchorage grounds—(1..., power plant, oil terminal, marine terminal, munitions plant, military or naval arsenal or depot...

33 CFR 110.132 - Rockland Harbor, Maine.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Rockland Harbor, Maine. 110.132... ANCHORAGE REGULATIONS Anchorage Grounds § 110.132 Rockland Harbor, Maine. (a) The anchorage grounds—(1..., power plant, oil terminal, marine terminal, munitions plant, military or naval arsenal or depot...

33 CFR 110.132 - Rockland Harbor, Maine.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Rockland Harbor, Maine. 110.132... ANCHORAGE REGULATIONS Anchorage Grounds § 110.132 Rockland Harbor, Maine. (a) The anchorage grounds—(1..., power plant, oil terminal, marine terminal, munitions plant, military or naval arsenal or depot...

DOCK2 regulates cell proliferation through Rac and ERK activation in B cell lymphoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Lei; Nishihara, Hiroshi, E-mail: nisihara@patho2.med.hokudai.ac.jp; Kimura, Taichi

2010-04-23

DOCK2; a member of the CDM protein family, regulates cell motility and cytokine production through the activation of Rac in mammalian hematopoietic cells and plays a pivotal role in the modulation of the immune system. Here we demonstrated the alternative function of DOCK2 in hematopoietic tumor cells, especially in terms of its association with the tumor progression. Immunostaining for DOCK2 in 20 cases of human B cell lymphoma tissue specimens including diffuse large B cell lymphoma and follicular lymphoma revealed the prominent expression of DOCK2 in all of the lymphoma cells. DOCK2-knockdown (KD) of the B cell lymphoma cell lines,more » Ramos and Raji, using the lentiviral shRNA system presented decreased cell proliferation compared to the control cells. Furthermore, the tumor formation of DOCK2-KD Ramos cell in nude mice was significantly abrogated. Western blotting analysis and pull-down assay using GST-PAK-RBD kimeric protein suggested the presence of DOCK2-Rac-ERK pathway regulating the cell proliferation of these lymphoma cells. This is the first report to clarify the prominent role of DOCK2 in hematopoietic malignancy.« less

Protein-protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring.

PubMed

Gong, Xinqi; Wang, Panwen; Yang, Feng; Chang, Shan; Liu, Bin; He, Hongqiu; Cao, Libin; Xu, Xianjin; Li, Chunhua; Chen, Weizu; Wang, Cunxin

2010-11-15

Protein-protein docking has made much progress in recent years, but challenges still exist. Here we present the application of our docking approach HoDock in CAPRI. In this approach, a binding site prediction is implemented to reduce docking sampling space and filter out unreasonable docked structures, and a network-based enhanced combinatorial scoring function HPNCscore is used to evaluate the decoys. The experimental information was combined with the predicted binding site to pick out the most likely key binding site residues. We applied the HoDock method in the recent rounds of the CAPRI experiments, and got good results as predictors on targets 39, 40, and 41. We also got good results as scorers on targets 35, 37, 40, and 41. This indicates that our docking approach can contribute to the progress of protein-protein docking methods and to the understanding of the mechanism of protein-protein interactions. © 2010 Wiley-Liss, Inc.

Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.

PubMed

Brylinski, Michal

2013-11-25

A common strategy for virtual screening considers a systematic docking of a large library of organic compounds into the target sites in protein receptors with promising leads selected based on favorable intermolecular interactions. Despite a continuous progress in the modeling of protein-ligand interactions for pharmaceutical design, important challenges still remain, thus the development of novel techniques is required. In this communication, we describe eSimDock, a new approach to ligand docking and binding affinity prediction. eSimDock employs nonlinear machine learning-based scoring functions to improve the accuracy of ligand ranking and similarity-based binding pose prediction, and to increase the tolerance to structural imperfections in the target structures. In large-scale benchmarking using the Astex/CCDC data set, we show that 53.9% (67.9%) of the predicted ligand poses have RMSD of <2 Å (<3 Å). Moreover, using binding sites predicted by recently developed eFindSite, eSimDock models ligand binding poses with an RMSD of 4 Å for 50.0-39.7% of the complexes at the protein homology level limited to 80-40%. Simulations against non-native receptor structures, whose mean backbone rearrangements vary from 0.5 to 5.0 Å Cα-RMSD, show that the ratio of docking accuracy and the estimated upper bound is at a constant level of ∼0.65. Pearson correlation coefficient between experimental and predicted by eSimDock Ki values for a large data set of the crystal structures of protein-ligand complexes from BindingDB is 0.58, which decreases only to 0.46 when target structures distorted to 3.0 Å Cα-RMSD are used. Finally, two case studies demonstrate that eSimDock can be customized to specific applications as well. These encouraging results show that the performance of eSimDock is largely unaffected by the deformations of ligand binding regions, thus it represents a practical strategy for across-proteome virtual screening using protein models. eSimDock is freely

Expedition 21 Docking

NASA Image and Video Library

2009-10-01

The entire crew onboard the International Space Station (ISS) can be seen on the center screen of the Mission Control Center Moscow in Korolev, Russia shortly after the successful docking of the Soyuz TMA-16 spacecraft with the International Space Station marking the start of Expedition 21 with Flight Engineer Jeffrey N. Williams, Expedition 21 Flight Engineer Maxim Suraev, and Spaceflight Participant Guy Laliberté, Friday, Oct. 2, 2009. Photo Credit: (NASA/Bill Ingalls)

Expedition 21 Docking

NASA Image and Video Library

2009-10-01

The entire crew onboard the International Space Station (ISS) can be seen on a screen of the Mission Control Center Moscow in Korolev, Russia shortly after the successful docking of the Soyuz TMA-16 spacecraft with the International Space Station marking the start of Expedition 21 with Flight Engineer Jeffrey N. Williams, Expedition 21 Flight Engineer Maxim Suraev, and Spaceflight Participant Guy Laliberté, Friday, Oct. 2, 2009. Photo Credit: (NASA/Bill Ingalls)

Expedition 24 Docks to ISS

NASA Image and Video Library

2010-06-17

Alexei Krasnov, Director of Manned Space Programs Department, ROSCOSMOS, answers a reporter’s question during a Soyuz post-docking press conference at the Russian Mission Control Center in Korolev, Russia on Friday, June 18, 2010. Photo Credit: (NASA/Carla Cioffi)

Comprehensive Conservation and Management Plan for Charlotte Harbor

EPA Pesticide Factsheets

This 2013 CCMP Update for Charlotte Harbor provides insight on the main priorities that the harbor is facing as well as research needed, restoration activities, legislative changes, and public outreach needs.

33 CFR 80.1116 - Redondo Harbor, CA.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Redondo Harbor, CA. 80.1116 Section 80.1116 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1116 Redondo Harbor, CA. A line drawn from...

33 CFR 80.1116 - Redondo Harbor, CA.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Redondo Harbor, CA. 80.1116 Section 80.1116 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1116 Redondo Harbor, CA. A line drawn from...

33 CFR 80.1108 - Oceanside Harbor, CA.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Oceanside Harbor, CA. 80.1108 Section 80.1108 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1108 Oceanside Harbor, CA. A line drawn from...

33 CFR 80.1108 - Oceanside Harbor, CA.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Oceanside Harbor, CA. 80.1108 Section 80.1108 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1108 Oceanside Harbor, CA. A line drawn from...

33 CFR 80.1134 - Monterey Harbor, CA.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Monterey Harbor, CA. 80.1134 Section 80.1134 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1134 Monterey Harbor, CA. A line drawn from...

33 CFR 80.1134 - Monterey Harbor, CA.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Monterey Harbor, CA. 80.1134 Section 80.1134 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1134 Monterey Harbor, CA. A line drawn from...

33 CFR 80.1134 - Monterey Harbor, CA.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Monterey Harbor, CA. 80.1134 Section 80.1134 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1134 Monterey Harbor, CA. A line drawn from...

33 CFR 80.1116 - Redondo Harbor, CA.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Redondo Harbor, CA. 80.1116 Section 80.1116 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1116 Redondo Harbor, CA. A line drawn from...

33 CFR 80.1134 - Monterey Harbor, CA.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Monterey Harbor, CA. 80.1134 Section 80.1134 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1134 Monterey Harbor, CA. A line drawn from...

33 CFR 80.1108 - Oceanside Harbor, CA.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Oceanside Harbor, CA. 80.1108 Section 80.1108 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1108 Oceanside Harbor, CA. A line drawn from...

33 CFR 80.1108 - Oceanside Harbor, CA.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Oceanside Harbor, CA. 80.1108 Section 80.1108 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1108 Oceanside Harbor, CA. A line drawn from...

33 CFR 80.1116 - Redondo Harbor, CA.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Redondo Harbor, CA. 80.1116 Section 80.1116 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1116 Redondo Harbor, CA. A line drawn from...

33 CFR 80.1116 - Redondo Harbor, CA.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Redondo Harbor, CA. 80.1116 Section 80.1116 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1116 Redondo Harbor, CA. A line drawn from...

33 CFR 80.1134 - Monterey Harbor, CA.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Monterey Harbor, CA. 80.1134 Section 80.1134 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1134 Monterey Harbor, CA. A line drawn from...

33 CFR 80.1108 - Oceanside Harbor, CA.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Oceanside Harbor, CA. 80.1108 Section 80.1108 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1108 Oceanside Harbor, CA. A line drawn from...

33 CFR 110.82 - Charlevoix Harbor, Mich.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Charlevoix Harbor, Mich. 110.82 Section 110.82 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.82 Charlevoix Harbor, Mich. The waters on the north side...

33 CFR 110.50 - Stonington Harbor, Conn.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Stonington Harbor, Conn. 110.50 Section 110.50 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.50 Stonington Harbor, Conn. (a) Area No. 1. Beginning at...

33 CFR 110.82 - Charlevoix Harbor, Mich.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Charlevoix Harbor, Mich. 110.82 Section 110.82 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.82 Charlevoix Harbor, Mich. The waters on the north side...

33 CFR 110.50 - Stonington Harbor, Conn.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Stonington Harbor, Conn. 110.50 Section 110.50 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.50 Stonington Harbor, Conn. (a) Area No. 1. Beginning at...

33 CFR 110.82 - Charlevoix Harbor, Mich.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Charlevoix Harbor, Mich. 110.82 Section 110.82 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.82 Charlevoix Harbor, Mich. The waters on the north side...

33 CFR 110.82 - Charlevoix Harbor, Mich.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Charlevoix Harbor, Mich. 110.82 Section 110.82 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.82 Charlevoix Harbor, Mich. The waters on the north side...

33 CFR 110.50 - Stonington Harbor, Conn.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Stonington Harbor, Conn. 110.50 Section 110.50 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.50 Stonington Harbor, Conn. (a) Area No. 1. Beginning at...

33 CFR 110.50 - Stonington Harbor, Conn.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Stonington Harbor, Conn. 110.50 Section 110.50 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.50 Stonington Harbor, Conn. (a) Area No. 1. Beginning at...

33 CFR 110.82 - Charlevoix Harbor, Mich.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Charlevoix Harbor, Mich. 110.82 Section 110.82 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.82 Charlevoix Harbor, Mich. The waters on the north side...

33 CFR 110.50 - Stonington Harbor, Conn.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Stonington Harbor, Conn. 110.50 Section 110.50 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.50 Stonington Harbor, Conn. (a) Area No. 1. Beginning at...

33 CFR 110.142 - Nantucket Harbor, Mass.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Nantucket Harbor, Mass. 110.142 Section 110.142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.142 Nantucket Harbor, Mass. (a) The anchorage grounds. In the...

33 CFR 110.138 - Boston Harbor, Mass.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Boston Harbor, Mass. 110.138 Section 110.138 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.138 Boston Harbor, Mass. (a) The anchorage grounds—(1) Bird...

33 CFR 110.142 - Nantucket Harbor, Mass.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Nantucket Harbor, Mass. 110.142 Section 110.142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.142 Nantucket Harbor, Mass. (a) The anchorage grounds. In the...

16 CFR 312.11 - Safe harbor programs.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 1 2014-01-01 2014-01-01 false Safe harbor programs. 312.11 Section 312.11 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS CHILDREN'S ONLINE PRIVACY PROTECTION RULE § 312.11 Safe harbor programs. (a) In general. Industry groups or other persons...

Space Tug Docking Study. Volume 1: Executive Summary

NASA Technical Reports Server (NTRS)

1976-01-01

Results of a detailed systems analysis of the entire rendezvous and docking operation to be performed by the all-up space tug are presented. Specific areas investigated include: generating of operational requirements and a data base of candidate operational techniques and subsystem mechanizations; selection and ranking of integrated system designs capable of meeting the requirements generated; and definition of this simulation/demonstration program required to select and prove the most effective manual, autonomous, and hybrid rendezvous and docking systems.

36. ORE DOCK, LOOKING WEST. HULETT UNLOADERS AWAIT THE NEXT ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

36. ORE DOCK, LOOKING WEST. HULETT UNLOADERS AWAIT THE NEXT ORE BOAT. BY LATE WINTER, THE ORE STORAGE YARD SEEN AT LEFT WILL BE DEPLETED. - Pennsylvania Railway Ore Dock, Lake Erie at Whiskey Island, approximately 1.5 miles west of Public Square, Cleveland, Cuyahoga County, OH

Binding site and affinity prediction of general anesthetics to protein targets using docking.

PubMed

Liu, Renyu; Perez-Aguilar, Jose Manuel; Liang, David; Saven, Jeffery G

2012-05-01

The protein targets for general anesthetics remain unclear. A tool to predict anesthetic binding for potential binding targets is needed. In this study, we explored whether a computational method, AutoDock, could serve as such a tool. High-resolution crystal data of water-soluble proteins (cytochrome C, apoferritin, and human serum albumin), and a membrane protein (a pentameric ligand-gated ion channel from Gloeobacter violaceus [GLIC]) were used. Isothermal titration calorimetry (ITC) experiments were performed to determine anesthetic affinity in solution conditions for apoferritin. Docking calculations were performed using DockingServer with the Lamarckian genetic algorithm and the Solis and Wets local search method (http://www.dockingserver.com/web). Twenty general anesthetics were docked into apoferritin. The predicted binding constants were compared with those obtained from ITC experiments for potential correlations. In the case of apoferritin, details of the binding site and their interactions were compared with recent cocrystallization data. Docking calculations for 6 general anesthetics currently used in clinical settings (isoflurane, sevoflurane, desflurane, halothane, propofol, and etomidate) with known 50% effective concentration (EC(50)) values were also performed in all tested proteins. The binding constants derived from docking experiments were compared with known EC(50) values and octanol/water partition coefficients for the 6 general anesthetics. All 20 general anesthetics docked unambiguously into the anesthetic binding site identified in the crystal structure of apoferritin. The binding constants for 20 anesthetics obtained from the docking calculations correlate significantly with those obtained from ITC experiments (P = 0.04). In the case of GLIC, the identified anesthetic binding sites in the crystal structure are among the docking predicted binding sites, but not the top ranked site. Docking calculations suggest a most probable binding site

Erie Harbor, Pennsylvania, Channel Shoaling Analysis

DTIC Science & Technology

2011-07-01

Presque Isle is located on the southern shore of Lake Erie and shelters the federal harbor at Erie , Pennsylvania . The US Army...the evaluation of the shoaling and dredging of sediment materials from Erie Harbor as part of the Presque Isle , Pennsylvania 204 feasibility study...ERDC TR-11-4 1 1 Introduction Problem statement Presque Isle is located on the southern shore of Lake Erie , Pennsylvania at the city of Erie

Knowing when to give up: early-rejection stratagems in ligand docking

NASA Astrophysics Data System (ADS)

Skone, Gwyn; Voiculescu, Irina; Cameron, Stephen

2009-10-01

Virtual screening is an important resource in the drug discovery community, of which protein-ligand docking is a significant part. Much software has been developed for this purpose, largely by biochemists and those in related disciplines, who pursue ever more accurate representations of molecular interactions. The resulting tools, however, are very processor-intensive. This paper describes some initial results from a project to review computational chemistry techniques for docking from a non-chemistry standpoint. An abstract blueprint for protein-ligand docking using empirical scoring functions is suggested, and this is used to discuss potential improvements. By introducing computer science tactics such as lazy function evaluation, dramatic increases to throughput can and have been realized using a real-world docking program. Naturally, they can be extended to any system that approximately corresponds to the architecture outlined.

33 CFR 80.165 - New York Harbor.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false New York Harbor. 80.165 Section 80.165 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Atlantic Coast § 80.165 New York Harbor. A line drawn from East...

33 CFR 110.9 - Wells Harbor, Maine.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Section 110.9 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.9 Wells Harbor, Maine. (a) Anchorage “A”. All of the... approximately 5,800 sq. yards, encompassing the central portion of Wells Harbor. (b) Anchorage “B”. All of the...

12 CFR 350.11 - Safe harbor provision.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Safe harbor provision. 350.11 Section 350.11 Banks and Banking FEDERAL DEPOSIT INSURANCE CORPORATION REGULATIONS AND STATEMENTS OF GENERAL POLICY DISCLOSURE OF FINANCIAL AND OTHER INFORMATION BY FDIC-INSURED STATE NONMEMBER BANKS § 350.11 Safe harbor...

33 CFR 110.250 - St. Thomas Harbor, Charlotte Amalie, V.I.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false St. Thomas Harbor, Charlotte... SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.250 St. Thomas Harbor, Charlotte Amalie... move promptly upon notification by the Harbor Master. (4) The harbor regulations for the Port of St...

1. Southwest front, dock no. 491. Aircraft tail extends through ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. Southwest front, dock no. 491. Aircraft tail extends through gasket in center hangar doors. View to east. - Offutt Air Force Base, Looking Glass Airborne Command Post, Nose Docks, On either side of Hangar Access Apron at Northwest end of Project Looking Glass Historic District, Bellevue, Sarpy County, NE

Application of the docking program SOL for CSAR benchmark.

PubMed

Sulimov, Alexey V; Kutov, Danil C; Oferkin, Igor V; Katkova, Ekaterina V; Sulimov, Vladimir B

2013-08-26

This paper is devoted to results obtained by the docking program SOL and the post-processing program DISCORE at the CSAR benchmark. SOL and DISCORE programs are described. SOL is the original docking program developed on the basis of the genetic algorithm, MMFF94 force field, rigid protein, precalculated energy grid including desolvation in the frame of simplified GB model, vdW, and electrostatic interactions and taking into account the ligand internal strain energy. An important SOL feature is the single- or multi-processor performance for up to hundreds of CPUs. DISCORE improves the binding energy scoring by the local energy optimization of the ligand docked pose and a simple linear regression on the base of available experimental data. The docking program SOL has demonstrated a good ability for correct ligand positioning in the active sites of the tested proteins in most cases of CSAR exercises. SOL and DISCORE have not demonstrated very exciting results on the protein-ligand binding free energy estimation. Nevertheless, for some target proteins, SOL and DISCORE were among the first in prediction of inhibition activity. Ways to improve SOL and DISCORE are discussed.

Dock and Pak regulate olfactory axon pathfinding in Drosophila.

PubMed

Ang, Lay-Hong; Kim, Jenny; Stepensky, Vitaly; Hing, Huey

2003-04-01

The convergence of olfactory axons expressing particular odorant receptor (Or) genes on spatially invariant glomeruli in the brain is one of the most dramatic examples of precise axon targeting in developmental neurobiology. The cellular and molecular mechanisms by which olfactory axons pathfind to their targets are poorly understood. We report here that the SH2/SH3 adapter Dock and the serine/threonine kinase Pak are necessary for the precise guidance of olfactory axons. Using antibody localization, mosaic analyses and cell-type specific rescue, we observed that Dock and Pak are expressed in olfactory axons and function autonomously in olfactory neurons to regulate the precise wiring of the olfactory map. Detailed analyses of the mutant phenotypes in whole mutants and in small multicellular clones indicate that Dock and Pak do not control olfactory neuron (ON) differentiation, but specifically regulate multiple aspects of axon trajectories to guide them to their cognate glomeruli. Structure/function studies show that Dock and Pak form a signaling pathway that mediates the response of olfactory axons to guidance cues in the developing antennal lobe (AL). Our findings therefore identify a central signaling module that is used by ONs to project to their cognate glomeruli.

Comparison of neural histomorphology in tail tips from pigs docked using clippers or cautery iron.

PubMed

Kells, N J; Beausoleil, N J; Johnson, C B; Sutherland, M A; Morrison, R S; Roe, W

2017-07-01

Tail docking of pigs is commonly performed to reduce the incidence of unwanted tail-biting behaviour. Two docking methods are commonly used: blunt trauma cutting (i.e. using side clippers), or cutting and concurrent cauterisation using a hot cautery iron. A potential consequence of tail amputation is the development of neuromas at the docking site. Neuromas have been linked to neuropathic pain, which can influence the longer-term welfare of affected individuals. To determine whether method of tail docking influences the extent of neuroma formation, 75 pigs were allocated to one of three treatments at birth: tail docked using clippers; tail docked using cautery iron; tail left intact. Tail docking was performed at 2 days of age and pigs were kept under conventional conditions until slaughter at 21 weeks of age. Tails were removed following slaughter and subjected to histological examination. Nerve histomorphology was scored according to the following scale: 1=discrete well-organised nerve bundles; 2=moderate neural proliferation and disorganisation affecting more than half of the circumference of the tail; 3=marked neural proliferation to form almost continuous disorganised bundles or non-continuous enlarged bundles compressing the surrounding connective tissue. Scores of 2 or 3 indicated neuroma formation. Scores were higher in docked pigs than undocked pigs (P<0.001), but did not differ between pigs docked using clippers and those docked using cautery (P=0.23). The results indicate that tail docking using either clippers or cautery results in neuroma formation, thus having the potential to affect long-term pig welfare.

Cosmetic tail docking: an overview of abuse and report of an interesting case.

PubMed

Eyarefe, Oghenemega David; Oguntoye, Cecilia O

2016-02-29

This paper presents an overview of the global controversies surrounding cosmetic tail docking in puppies, some observed inconsistent practices among dog breeders and Veterinarians in West Africa, and the need for the African Veterinary Profession to take a decisive position on the cosmetic docking procedure. An interesting report of observed complications associated with cosmetic tail docking in a 3 week old male Boerboel is reported alongside the management of the ensuing complications. This paper highlights the still prevalent practice of cosmetic tail docking and seeks to enlighten clinicians towards stemming its abuse in Africa.

Laser space rendezvous and docking tradeoff

NASA Technical Reports Server (NTRS)

Adelman, S.; Levinson, S.; Raber, P.; Weindling, F.

1974-01-01

A spaceborne laser radar (LADAR) was configured to meet the requirements for rendezvous and docking with a cooperative object in synchronous orbit. The LADAR, configurated using existing pulsed CO2 laser technology and a 1980 system technology baseline, is well suited for the envisioned space tug missions. The performance of a family of candidate LADARS was analyzed. Tradeoff studies as a function of size, weight, and power consumption were carried out for maximum ranges of 50, 100, 200, and 300 nautical miles. The investigation supports the original contention that a rendezvous and docking LADAR can be constructed to offer a cost effective and reliable solution to the envisioned space missions. In fact, the CO2 ladar system offers distinct advantages over other candidate systems.

33 CFR 117.802 - New Rochelle Harbor.

Code of Federal Regulations, 2010 CFR

2010-07-01

... DRAWBRIDGE OPERATION REGULATIONS Specific Requirements New York § 117.802 New Rochelle Harbor. (a) The draw of the Glen Island Bridge, mile 0.8, at New Rochelle, New York, shall open on signal, except as... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false New Rochelle Harbor. 117.802...

View of the Pirs Docking Compartment approaching the ISS during Expedition Three

NASA Image and Video Library

2001-09-17

ISS003-E-5620 (16 September 2001) --- The Russian Docking Compartment, named Pirs (the Russian word for pier), is only seconds away from docking with the International Space Station (ISS). One of the Expedition Three crew members, using a digital still camera with a 35mm lens, recorded the image from onboard the orbital outpost. The vehicle was launched on September 14, 2001 and docking occurred on September 16.

A molecular docking study of phytochemical estrogen mimics from dietary herbal supplements.

PubMed

Powers, Chelsea N; Setzer, William N

2015-01-01

The purpose of this study is to use a molecular docking approach to identify potential estrogen mimics or anti-estrogens in phytochemicals found in popular dietary herbal supplements. In this study, 568 phytochemicals found in 17 of the most popular herbal supplements sold in the United States were built and docked with two isoforms of the estrogen receptor, ERα and ERβ (a total of 27 different protein crystal structures). The docking results revealed six strongly docking compounds in Echinacea, three from milk thistle (Silybum marianum), three from Gingko biloba, one from Sambucus nigra, none from maca (Lepidium meyenii), five from chaste tree (Vitex agnus-castus), two from fenugreek (Trigonella foenum-graecum), and two from Rhodiola rosea. Notably, of the most popular herbal supplements for women, there were numerous compounds that docked strongly with the estrogen receptor: Licorice (Glycyrrhiza glabra) had a total of 26 compounds strongly docking to the estrogen receptor, 15 with wild yam (Dioscorea villosa), 11 from black cohosh (Actaea racemosa), eight from muira puama (Ptychopetalum olacoides or P. uncinatum), eight from red clover (Trifolium pratense), three from damiana (Turnera aphrodisiaca or T. diffusa), and three from dong quai (Angelica sinensis). Of possible concern were the compounds from men's herbal supplements that exhibited strong docking to the estrogen receptor: Gingko biloba had three compounds, gotu kola (Centella asiatica) had two, muira puama (Ptychopetalum olacoides or P. uncinatum) had eight, and Tribulus terrestris had six compounds. This molecular docking study has revealed that almost all popular herbal supplements contain phytochemical components that may bind to the human estrogen receptor and exhibit selective estrogen receptor modulation. As such, these herbal supplements may cause unwanted side effects related to estrogenic activity.

A benchmark testing ground for integrating homology modeling and protein docking.

PubMed

Bohnuud, Tanggis; Luo, Lingqi; Wodak, Shoshana J; Bonvin, Alexandre M J J; Weng, Zhiping; Vajda, Sandor; Schueler-Furman, Ora; Kozakov, Dima

2017-01-01

Protein docking procedures carry out the task of predicting the structure of a protein-protein complex starting from the known structures of the individual protein components. More often than not, however, the structure of one or both components is not known, but can be derived by homology modeling on the basis of known structures of related proteins deposited in the Protein Data Bank (PDB). Thus, the problem is to develop methods that optimally integrate homology modeling and docking with the goal of predicting the structure of a complex directly from the amino acid sequences of its component proteins. One possibility is to use the best available homology modeling and docking methods. However, the models built for the individual subunits often differ to a significant degree from the bound conformation in the complex, often much more so than the differences observed between free and bound structures of the same protein, and therefore additional conformational adjustments, both at the backbone and side chain levels need to be modeled to achieve an accurate docking prediction. In particular, even homology models of overall good accuracy frequently include localized errors that unfavorably impact docking results. The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations. Here we present a benchmark dataset that should help to explore and solve combined modeling and docking problems. This dataset comprises a subset of the experimentally solved 'target' complexes from the widely used Docking Benchmark from the Weng Lab (excluding antibody-antigen complexes). This subset is extended to include the structures from the PDB related to those of the individual components of each complex, and hence represent potential templates for investigating and benchmarking integrated homology modeling and docking approaches. Template sets can be dynamically customized by specifying ranges in sequence similarity and in

Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity.

PubMed

de Molfetta, Fábio Alberto; de Freitas, Renato Ferreira; da Silva, Albérico Borges Ferreira; Montanari, Carlos Alberto

2009-10-01

In this work, two different docking programs were used, AutoDock and FlexX, which use different types of scoring functions and searching methods. The docking poses of all quinone compounds studied stayed in the same region in the trypanothione reductase. This region is a hydrophobic pocket near to Phe396, Pro398 and Leu399 amino acid residues. The compounds studied displays a higher affinity in trypanothione reductase (TR) than glutathione reductase (GR), since only two out of 28 quinone compounds presented more favorable docking energy in the site of human enzyme. The interaction of quinone compounds with the TR enzyme is in agreement with other studies, which showed different binding sites from the ones formed by cysteines 52 and 58. To verify the results obtained by docking, we carried out a molecular dynamics simulation with the compounds that presented the highest and lowest docking energies. The results showed that the root mean square deviation (RMSD) between the initial and final pose were very small. In addition, the hydrogen bond pattern was conserved along the simulation. In the parasite enzyme, the amino acid residues Leu399, Met400 and Lys402 are replaced in the human enzyme by Met406, Tyr407 and Ala409, respectively. In view of the fact that Leu399 is an amino acid of the Z site, this difference could be explored to design selective inhibitors of TR.

External airlock assembly/Mir docking system being loaded

NASA Image and Video Library

1994-11-15

S95-00057 (15 Nov 1994) --- In Rockwell's Building 290 at Downey, California, the external airlock assembly/Mir docking system is rotated into position for crating up for shipment to the Kennedy Space Center (KSC) in Florida. Jointly developed by Rockwell and RSC Energia, the external airlock assembly and Mir docking system will be mounted in the cargo bay of the Space Shuttle Atlantis to enable the shuttle to link up to Russia's Mir space station. The docking system contains hooks and latches compatible with the system currently housed on the Mir's Krystall module, to which Atlantis will attach for the first time next spring. STS-71 will carry two Russian cosmonauts, who will replace a three-man crew aboard Mir including Norman E. Thagard, a NASA astronaut. The combined 10-person crew will conduct almost five days of joint life sciences investigations both aboard Mir and in the Space Shuttle Atlantis's Spacelab module.

Orbiter Docking System/Spacelab-Mir Module in Atlantis

NASA Technical Reports Server (NTRS)

1995-01-01

The STS-71 mission payload is in its final flight configuration after integration into the payload bay of the Space Shuttle orbiter Atlantis and prior to payload bay door closing and rollover of the spaceplane from Orbiter Processing Facility Bay 3 to the Vehicle Assembly Building. In the foreground is the Orbiter Docking System (ODS) that is topped with the red Russian- built Androgynous Peripheral Docking System (APDS). During the 11-day mission, the APDS will lock together with a similar system on the Russian Mir Space Station so that the two spacecraft can remain docked together for four days. The ODS features an airlock that will provide access to and from both the Mir and orbiter for the U.S. and Russian flight crews. A Spacelab transfer tunnel runs from the ODS to the Spacelab-Mir module, where joint U.S. medical experiments will be conducted during the 11-day spaceflight.

DOT2: Macromolecular Docking With Improved Biophysical Models

PubMed Central

Roberts, Victoria A.; Thompson, Elaine E.; Pique, Michael E.; Perez, Martin S.; Eyck, Lynn Ten

2015-01-01

Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate a complete list of favorable candidate configu-rations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions, and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. PMID:23695987

GPU Optimizations for a Production Molecular Docking Code*

PubMed Central

Landaverde, Raphael; Herbordt, Martin C.

2015-01-01

Modeling molecular docking is critical to both understanding life processes and designing new drugs. In previous work we created the first published GPU-accelerated docking code (PIPER) which achieved a roughly 5× speed-up over a contemporaneous 4 core CPU. Advances in GPU architecture and in the CPU code, however, have since reduced this relalative performance by a factor of 10. In this paper we describe the upgrade of GPU PIPER. This required an entire rewrite, including algorithm changes and moving most remaining non-accelerated CPU code onto the GPU. The result is a 7× improvement in GPU performance and a 3.3× speedup over the CPU-only code. We find that this difference in time is almost entirely due to the difference in run times of the 3D FFT library functions on CPU (MKL) and GPU (cuFFT), respectively. The GPU code has been integrated into the ClusPro docking server which has over 4000 active users. PMID:26594667

GPU Optimizations for a Production Molecular Docking Code.

PubMed

Landaverde, Raphael; Herbordt, Martin C

2014-09-01

Modeling molecular docking is critical to both understanding life processes and designing new drugs. In previous work we created the first published GPU-accelerated docking code (PIPER) which achieved a roughly 5× speed-up over a contemporaneous 4 core CPU. Advances in GPU architecture and in the CPU code, however, have since reduced this relalative performance by a factor of 10. In this paper we describe the upgrade of GPU PIPER. This required an entire rewrite, including algorithm changes and moving most remaining non-accelerated CPU code onto the GPU. The result is a 7× improvement in GPU performance and a 3.3× speedup over the CPU-only code. We find that this difference in time is almost entirely due to the difference in run times of the 3D FFT library functions on CPU (MKL) and GPU (cuFFT), respectively. The GPU code has been integrated into the ClusPro docking server which has over 4000 active users.

Decadal Changes In Benthic Community Measures In New York Harbor

EPA Science Inventory

Monitoring in New York Harbor, NY, as part of the Regional Environmental Monitoring and Assessment Program has spanned a decade, and includes habitat and water quality measures and sediment contaminant levels from four sub-basins (Upper NY Harbor, Lower NY Harbor, Newark Bay, and...

Sediment resuspension characteristics in Baltimore Harbor, Maryland

USGS Publications Warehouse

Maa, J.P.-Y.; Sanford, L.; Halka, J.P.

1998-01-01

Critical bed shear stress for sediment resuspension and sediment erosion rate were measured in-situ at sites from inner to outer Baltimore Harbor using the VIMS Sea Carousel. Clay mineral contents and biological conditions were almost the same at the four study sites. The experimental results indicated that the erosion rate increased from the outer harbor toward the inner harbor with a maximum difference of about 10 times at an excess bed shear stress of 0.1 Pa. The measured critical bed shear stress strongly depended on the existence of a fluff layer. It was approximately 0.05 Pa if a fluff layer existed, and increases to about 0.1 Pa in the absence of a fluff layer.

Vinogradov practices docking procedures of the Progress 21 in the SM during Expedition 13

NASA Image and Video Library

2006-04-26

ISS013-E-10225 (26 April 2006) --- Cosmonaut Pavel V. Vinogradov, Expedition 13 commander representing Russia's Federal Space Agency, practices docking procedures with the TORU teleoperated control system in the Zvezda Service Module of the International Space Station in preparation for the docking of the Progress 21 spacecraft. Vinogradov, using the Simvol-TS screen and hand controllers, could manually dock the Progress to the station in the event of a failure of the Kurs automated docking system.

Polycyclic aromatic hydrocarbons and trace elements bounded to airborne PM10 in the harbor of Volos, Greece: Implications for the impact of harbor activities

NASA Astrophysics Data System (ADS)

Manoli, E.; Chelioti-Chatzidimitriou, A.; Karageorgou, K.; Kouras, A.; Voutsa, D.; Samara, C.; Kampanos, I.

2017-10-01

Harbors are often characterized by high levels of air pollutants that are emitted from ship traffic and other harbor activities. In the present study, the concentrations of Polycyclic Aromatic Hydrocarbons (PAHs) and trace elements (As, Cd, Ni, Pb, Cr, Mn, Zn, and Fe) bounded to the inhalable particulate matter PM10 were studied in the harbor of Volos, central Greece, during a 2-year period (2014-2015). Seasonal and daily variations were investigated. Moreover, total carcinogenic and mutagenic activities of PAHs were calculated. The effect of major wind sectors (sea, city, industrial, harbor) was estimated to assess the potential contribution of ship traffic and harbor activities, such as scrap metal handling operations. Results showed that the harbor sector (calm winds ≤ 0.5 m s-1) was associated with the highest concentrations of PM10. The harbor sector was also associated with relatively increased levels of trace elements (As, Fe, Cr, Mn, Ni), however the effect of this sector was lower than the corresponding effect of the industrial wind sector. The sea sector showed only a slight increase in B[a]Py and Σ12PAHs, whereas the highest increasing effect for PAHs and traffic-related elements, such as Pb and Zn, was evidenced for the city sector.

GEMINI-TITAN (GT)-9 - EARTH-SKY - AUGMENTED TARGET DOCKING ADAPTER (ATDA) - MSC

NASA Image and Video Library

1966-06-06

S66-37923 (3 June 1966) --- The Augmented Target Docking Adapter (ATDA) as seen from the Gemini-9 spacecraft during one of their three rendezvous in space. The ATDA and Gemini-9 spacecraft are 66.5 feet apart. Failure of the docking adapter protective cover to fully separate on the ATDA prevented the docking of the two spacecraft. The ATDA was described by the Gemini-9 crew as an "angry alligator." Photo credit: NASA

Spectroscopic, molecular docking and structural activity studies of (E)-N‧-(substituted benzylidene/methylene) isonicotinohydrazide derivatives for DNA binding and their biological screening

NASA Astrophysics Data System (ADS)

Arshad, Nasima; Perveen, Fouzia; Saeed, Aamer; Channar, Pervaiz Ali; Farooqi, Shahid Iqbal; Larik, Fayaz Ali; Ismail, Hammad; Mirza, Bushra

2017-07-01

Acid catalyzed condensation of isoniazid with a number of suitably substituted aromatic and heterocyclic aldehydes was carried out in dry ethanol to afford the title (E)-N‧-(substituted benzylidene/methylene) isonicotinohydrazides (SF 1 - SF 4) in good yields. These compounds were characterized and further investigated for their binding with ds.DNA using UV- spectroscopy and molecular docking and for antitumor and antimicrobial potentials. A good correlation was found among spectroscopic, theoretical and biological results. UV- spectra in the presence of DNA concentrations and their data interpretation in terms binding constant "Kb" and free energy change (ΔG) provided evidences for the significant and spontaneous binding of the compounds with DNA. Molecular docking studies and structural analysis further supported the UV-findings and indicated that the modes of interactions between bromo- (SF 1) and flouro- (SF 4) substituted isonicotinohydrazides is intercalation while methoxy- (SF 2) and hydroxy- (SF 3) substituted isonicotinohydrazides interact with DNA helix via groove binding. SF 1 exhibited comparatively higher Kb value (UV-; 8.07 × 103 M-1, docking; 8.11 × 103 M-1) which inferred that the respective compound muddles to DNA most powerfully. SF 1 has shown the lowest IC50 (345.3 μg/mL) value among all the compounds indicating its comparatively highest activity towards tumor inhibition. None of the compound has shown perceptible antibacterial and antifungal activities.

Protein-ligand docking using fitness learning-based artificial bee colony with proximity stimuli.

PubMed

Uehara, Shota; Fujimoto, Kazuhiro J; Tanaka, Shigenori

2015-07-07

Protein-ligand docking is an optimization problem, which aims to identify the binding pose of a ligand with the lowest energy in the active site of a target protein. In this study, we employed a novel optimization algorithm called fitness learning-based artificial bee colony with proximity stimuli (FlABCps) for docking. Simulation results revealed that FlABCps improved the success rate of docking, compared to four state-of-the-art algorithms. The present results also showed superior docking performance of FlABCps, in particular for dealing with highly flexible ligands and proteins with a wide and shallow binding pocket.

33 CFR 110.138 - Boston Harbor, Mass.

Code of Federal Regulations, 2012 CFR

2012-07-01

... line running due north from Old Harbor Buoy 4 to the shore line at City Point. (5) Explosives anchorage... beacon on top of the Boston Custom House tower; and thence to the point of beginning. (2) President Roads... adjacent land; on the east by a line between Castle Rocks Fog Signal Light and Old Harbor Shoal Buoy 2; on...

33 CFR 110.138 - Boston Harbor, Mass.

Code of Federal Regulations, 2013 CFR

2013-07-01

... line running due north from Old Harbor Buoy 4 to the shore line at City Point. (5) Explosives anchorage... beacon on top of the Boston Custom House tower; and thence to the point of beginning. (2) President Roads... adjacent land; on the east by a line between Castle Rocks Fog Signal Light and Old Harbor Shoal Buoy 2; on...

33 CFR 110.138 - Boston Harbor, Mass.

Code of Federal Regulations, 2014 CFR

2014-07-01

... line running due north from Old Harbor Buoy 4 to the shore line at City Point. (5) Explosives anchorage... beacon on top of the Boston Custom House tower; and thence to the point of beginning. (2) President Roads... adjacent land; on the east by a line between Castle Rocks Fog Signal Light and Old Harbor Shoal Buoy 2; on...

Binding Site and Affinity Prediction of General Anesthetics to Protein Targets Using Docking

PubMed Central

Liu, Renyu; Perez-Aguilar, Jose Manuel; Liang, David; Saven, Jeffery G.

2012-01-01

Background The protein targets for general anesthetics remain unclear. A tool to predict anesthetic binding for potential binding targets is needed. In this study, we explore whether a computational method, AutoDock, could serve as such a tool. Methods High-resolution crystal data of water soluble proteins (cytochrome C, apoferritin and human serum albumin), and a membrane protein (a pentameric ligand-gated ion channel from Gloeobacter violaceus, GLIC) were used. Isothermal titration calorimetry (ITC) experiments were performed to determine anesthetic affinity in solution conditions for apoferritin. Docking calculations were performed using DockingServer with the Lamarckian genetic algorithm and the Solis and Wets local search method (https://www.dockingserver.com/web). Twenty general anesthetics were docked into apoferritin. The predicted binding constants are compared with those obtained from ITC experiments for potential correlations. In the case of apoferritin, details of the binding site and their interactions were compared with recent co-crystallization data. Docking calculations for six general anesthetics currently used in clinical settings (isoflurane, sevoflurane, desflurane, halothane, propofol, and etomidate) with known EC50 were also performed in all tested proteins. The binding constants derived from docking experiments were compared with known EC50s and octanol/water partition coefficients for the six general anesthetics. Results All 20 general anesthetics docked unambiguously into the anesthetic binding site identified in the crystal structure of apoferritin. The binding constants for 20 anesthetics obtained from the docking calculations correlate significantly with those obtained from ITC experiments (p=0.04). In the case of GLIC, the identified anesthetic binding sites in the crystal structure are among the docking predicted binding sites, but not the top ranked site. Docking calculations suggest a most probable binding site located in the

Gemini Capsule and Rendezvous Docking Simulator

NASA Image and Video Library

1962-12-19

Practicing with a full-scale model of the Gemini Capsule in Langley's Rendezvous Docking Simulator. -- Caption and photograph published in Winds of Change, 75th Anniversary NASA publication, (page 89), by James Schultz.

Postprocessing of docked protein-ligand complexes using implicit solvation models.

PubMed

Lindström, Anton; Edvinsson, Lotta; Johansson, Andreas; Andersson, C David; Andersson, Ida E; Raubacher, Florian; Linusson, Anna

2011-02-28

Molecular docking plays an important role in drug discovery as a tool for the structure-based design of small organic ligands for macromolecules. Possible applications of docking are identification of the bioactive conformation of a protein-ligand complex and the ranking of different ligands with respect to their strength of binding to a particular target. We have investigated the effect of implicit water on the postprocessing of binding poses generated by molecular docking using MM-PB/GB-SA (molecular mechanics Poisson-Boltzmann and generalized Born surface area) methodology. The investigation was divided into three parts: geometry optimization, pose selection, and estimation of the relative binding energies of docked protein-ligand complexes. Appropriate geometry optimization afforded more accurate binding poses for 20% of the complexes investigated. The time required for this step was greatly reduced by minimizing the energy of the binding site using GB solvation models rather than minimizing the entire complex using the PB model. By optimizing the geometries of docking poses using the GB(HCT+SA) model then calculating their free energies of binding using the PB implicit solvent model, binding poses similar to those observed in crystal structures were obtained. Rescoring of these poses according to their calculated binding energies resulted in improved correlations with experimental binding data. These correlations could be further improved by applying the postprocessing to several of the most highly ranked poses rather than focusing exclusively on the top-scored pose. The postprocessing protocol was successfully applied to the analysis of a set of Factor Xa inhibitors and a set of glycopeptide ligands for the class II major histocompatibility complex (MHC) A(q) protein. These results indicate that the protocol for the postprocessing of docked protein-ligand complexes developed in this paper may be generally useful for structure-based design in drug discovery.

33 CFR 162.120 - Harbors on Lake Michigan.

Code of Federal Regulations, 2014 CFR

2014-07-01

.... (a) No vessel greater than 40 feet in length may exceed 8 miles per hour in the harbors of Michigan... Petoskey, Michigan. (b) No vessel greater than 40 feet in length may exceed 4 miles per hour in the harbors...

33 CFR 162.120 - Harbors on Lake Michigan.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (a) No vessel greater than 40 feet in length may exceed 8 miles per hour in the harbors of Michigan... Petroskey, Michigan. (b) No vessel greater than 40 feet in length may exceed 4 miles per hour in the harbors...

33 CFR 162.120 - Harbors on Lake Michigan.

Code of Federal Regulations, 2012 CFR

2012-07-01

.... (a) No vessel greater than 40 feet in length may exceed 8 miles per hour in the harbors of Michigan... Petoskey, Michigan. (b) No vessel greater than 40 feet in length may exceed 4 miles per hour in the harbors...

33 CFR 162.120 - Harbors on Lake Michigan.

Code of Federal Regulations, 2013 CFR

2013-07-01

.... (a) No vessel greater than 40 feet in length may exceed 8 miles per hour in the harbors of Michigan... Petoskey, Michigan. (b) No vessel greater than 40 feet in length may exceed 4 miles per hour in the harbors...

Kinetics of DNA-mediated docking reactions between vesicles tethered to supported lipid bilayers

PubMed Central

Chan, Yee-Hung M.; Lenz, Peter; Boxer, Steven G.

2007-01-01

Membrane–membrane recognition and binding are crucial in many biological processes. We report an approach to studying the dynamics of such reactions by using DNA-tethered vesicles as a general scaffold for displaying membrane components. This system was used to characterize the docking reaction between two populations of tethered vesicles that display complementary DNA. Deposition of vesicles onto a supported lipid bilayer was performed by using a microfluidic device to prevent mixing of the vesicles in bulk during sample preparation. Once tethered onto the surface, vesicles mixed via two-dimensional diffusion. DNA-mediated docking of two reacting vesicles results in their colocalization after collision and their subsequent tandem motion. Individual docking events and population kinetics were observed via epifluorescence microscopy. A lattice-diffusion simulation was implemented to extract from experimental data the probability, Pdock, that a collision leads to docking. For individual vesicles displaying small numbers of docking DNA, Pdock shows a first-order relationship with copy number as well as a strong dependence on the DNA sequence. Both trends are explained by a model that includes both tethered vesicle diffusion on the supported bilayer and docking DNA diffusion over each vesicle's surface. These results provide the basis for the application of tethered vesicles to study other membrane reactions including protein-mediated docking and fusion. PMID:18025472

Expedition 21 Docking

NASA Image and Video Library

2009-10-01

Spaceflight Participant Guy Laliberté is in the foreground as the entire crew onboard the International Space Station (ISS) is seen on a screen in the Mission Control Center Moscow in Korolev, Russia shortly after the successful docking of the Soyuz TMA-16 spacecraft with the International Space Station marking the start of Expedition 21 with Flight Engineer Jeffrey N. Williams, Expedition 21 Flight Engineer Maxim Suraev, and Spaceflight Participant Guy Laliberté, Friday, Oct. 2, 2009. Photo Credit: (NASA/Bill Ingalls)

Simulation of carbohydrates, from molecular docking to dynamics in water.

PubMed

Sapay, Nicolas; Nurisso, Alessandra; Imberty, Anne

2013-01-01

Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field. Nowadays, main carbohydrates force fields are GLYCAM06, CHARMM36, and GROMOS 45A4. GLYCAM06 includes the largest choice of compounds and is compatible with the AMBER force fields and associated. Furthermore, AMBER includes tools for the implementation of new parameters. When looking at protein-carbohydrate interaction, the choice of the starting structure is of importance. Such complex can be sometimes obtained from the Protein Data Bank-although the stereochemistry of sugars may require some corrections. When no experimental data is available, molecular docking simulation is generally used to the obtain protein-carbohydrate complex coordinates. As molecular docking parameters are not specifically dedicated to carbohydrates, inaccuracies should be expected, especially for the docking of polysaccharides. This issue can be addressed at least partially by combining molecular docking with molecular dynamics simulation in water.

Ligand-protein docking using a quantum stochastic tunneling optimization method.

PubMed

Mancera, Ricardo L; Källblad, Per; Todorov, Nikolay P

2004-04-30

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 858-864, 2004

Centrosome docking at the immunological synapse is controlled by Lck signaling

PubMed Central

Tsun, Andy; Qureshi, Ihjaaz; Stinchcombe, Jane C.; Jenkins, Misty R.; de la Roche, Maike; Kleczkowska, Joanna; Zamoyska, Rose

2011-01-01

Docking of the centrosome at the plasma membrane directs lytic granules to the immunological synapse. To identify signals controlling centrosome docking at the synapse, we have studied cytotoxic T lymphocytes (CTLs) in which expression of the T cell receptor–activated tyrosine kinase Lck is ablated. In the absence of Lck, the centrosome is able to translocate around the nucleus toward the immunological synapse but is unable to dock at the plasma membrane. Lytic granules fail to polarize and release their contents, and target cells are not killed. In CTLs deficient in both Lck and the related tyrosine kinase Fyn, centrosome translocation is impaired, and the centrosome remains on the distal side of the nucleus relative to the synapse. These results show that repositioning of the centrosome in CTLs involves at least two distinct steps, with Lck signaling required for the centrosome to dock at the plasma membrane. PMID:21339332

Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.