DockoMatic: automated peptide analog creation for high throughput virtual screening.

PubMed

Jacob, Reed B; Bullock, Casey W; Andersen, Tim; McDougal, Owen M

2011-10-01

The purpose of this manuscript is threefold: (1) to describe an update to DockoMatic that allows the user to generate cyclic peptide analog structure files based on protein database (pdb) files, (2) to test the accuracy of the peptide analog structure generation utility, and (3) to evaluate the high throughput capacity of DockoMatic. The DockoMatic graphical user interface interfaces with the software program Treepack to create user defined peptide analogs. To validate this approach, DockoMatic produced cyclic peptide analogs were tested for three-dimensional structure consistency and binding affinity against four experimentally determined peptide structure files available in the Research Collaboratory for Structural Bioinformatics database. The peptides used to evaluate this new functionality were alpha-conotoxins ImI, PnIA, and their published analogs. Peptide analogs were generated by DockoMatic and tested for their ability to bind to X-ray crystal structure models of the acetylcholine binding protein originating from Aplysia californica. The results, consisting of more than 300 simulations, demonstrate that DockoMatic predicts the binding energy of peptide structures to within 3.5 kcal mol(-1), and the orientation of bound ligand compares to within 1.8 Å root mean square deviation for ligand structures as compared to experimental data. Evaluation of high throughput virtual screening capacity demonstrated that Dockomatic can collect, evaluate, and summarize the output of 10,000 AutoDock jobs in less than 2 hours of computational time, while 100,000 jobs requires approximately 15 hours and 1,000,000 jobs is estimated to take up to a week. Copyright © 2011 Wiley Periodicals, Inc.

Automatic determination of trunk diameter, crown base and height of scots pine (Pinus Sylvestris L.) Based on analysis of 3D point clouds gathered from multi-station terrestrial laser scanning. (Polish Title: Automatyczne okreslanie srednicy pnia, podstawy korony oraz wysokosci sosny zwyczajnej (Pinus Silvestris L.) Na podstawie analiz chmur punktow 3D pochodzacych z wielostanowiskowego naziemnego skanowania laserowego)

NASA Astrophysics Data System (ADS)

Ratajczak, M.; Wężyk, P.

2015-12-01

Rapid development of terrestrial laser scanning (TLS) in recent years resulted in its recognition and implementation in many industries, including forestry and nature conservation. The use of the 3D TLS point clouds in the process of inventory of trees and stands, as well as in the determination of their biometric features (trunk diameter, tree height, crown base, number of trunk shapes), trees and lumber size (volume of trees) is slowly becoming a practice. In addition to the measurement precision, the primary added value of TLS is the ability to automate the processing of the clouds of points 3D in the direction of the extraction of selected features of trees and stands. The paper presents the original software (GNOM) for the automatic measurement of selected features of trees, based on the cloud of points obtained by the ground laser scanner FARO. With the developed algorithms (GNOM), the location of tree trunks on the circular research surface was specified and the measurement was performed; the measurement covered the DBH (l: 1.3m), further diameters of tree trunks at different heights of the tree trunk, base of the tree crown and volume of the tree trunk (the selection measurement method), as well as the tree crown. Research works were performed in the territory of the Niepolomice Forest in an unmixed pine stand (Pinussylvestris L.) on the circular surface with a radius of 18 m, within which there were 16 pine trees (14 of them were cut down). It was characterized by a two-storey and even-aged construction (147 years old) and was devoid of undergrowth. Ground scanning was performed just before harvesting. The DBH of 16 pine trees was specified in a fully automatic way, using the algorithm GNOM with an accuracy of +2.1%, as compared to the reference measurement by the DBH measurement device. The medium, absolute measurement error in the cloud of points - using semi-automatic methods "PIXEL" (between points) and PIPE (fitting the cylinder) in the FARO Scene 5.x., showed the error, 3.5% and 5.0%,.respectively The reference height was assumed as the measurement performed by the tape on the cut tree. The average error of automatic determination of the tree height by the algorithm GNOM based on the TLS point clouds amounted to 6.3% and was slightly higher than when using the manual method of measurements on profiles in the TerraScan (Terrasolid; the error of 5.6%). The relatively high value of the error may be mainly related to the small number of points TLS in the upper parts of crowns. The crown height measurement showed the error of +9.5%. The reference in this case was the tape measurement performed already on the trunks of cut pine trees. Processing the clouds of points by the algorithms GNOM for 16 analyzed trees took no longer than 10 min. (37 sec. /tree). The paper mainly showed the TLS measurement innovation and its high precision in acquiring biometric data in forestry, and at the same time also the further need to increase the degree of automation of processing the clouds of points 3D from terrestrial laser scanning.