a protein into domains is useful for obtaining an accurate structure and function determination. In previous-defined folded protein, , the native state . The resulting three-dimensional structure is determined by the amino a protein into domains is useful for more ...

mining the structure of protein and other large biological molecules. ... in a more accurate protein structure model (electron density map) being produced ...

of these proteins can then be determined, providing a cause for symptoms of a disease. If the structure and function for determining the structure of a protein. Protein samples are crystallized, and a fine beam of x to be able to accurately predict ...

Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data.

We use two co-evolving neural networks to determine new classes of protein secondary structure which are significantly more predictable from local amino sequence than the conventional secondary structure classification. Accurate prediction of the conventi...

protein, i.e., the native state [4]. The resulting three-dimensional structure is determined by the amino accurate structure and function determination. Methods for phylogenetic analyses or protein modeling cedex, FRANCE key words : amino acid; protein domain; side-chains; ...

The goal of computational protein structure prediction is to provide three-dimensional (3D) structures with resolution comparable to experimental results. Comparative modeling, which predicts the 3D structure of a protein based on its sequence similarity to homologous ...

Community structure is a topological property common to many networks. We present in this paper an efficient and accurate approach to detecting a community in a protein-protein interaction network from a given seed protein. Our experimental results show s...

We present a method, CamShift, for the rapid and accurate prediction of NMR chemical shifts from protein structures. The calculations performed by CamShift are based on an approximate expression of the chemical shifts in terms of polynomial functions of interatomic distances. Since these functions are very fast to compute and readily ...

� Structure of clusters � Structure of AFM tips � interfaces of ionic crystals � Protein folding #12;A wavelet to silicon clusters � Found numerous new low energy configurations for several midsize clusters � The energy for the first time the experimentally observed dissipation in AFM experiments #12;Ionic interfaces ...

Following the failure of a wide range of attempts to solve the crystal structure of M-PMV retroviral protease by molecular replacement, we challenged players of the protein folding game Foldit to produce accurate models of the protein. Remarkably, Foldit players were able to generate models of sufficient quality ...

1 Introduction In comparative structural biology studies, analyzing or predicting protein three-dimensional structure often begins with identifying patterns of amino acid substitution via protein sequence alignment. While the evolutionary informationobtained from alignments can provide insights into ...

Methods for determining protein structures using only chemical shift information are progressively becoming more accurate and reliable. A major problem, however, in the use of chemical shifts for the determination of the structures of protein complexes is that the changes in the chemical shifts ...

Protein crystals, routinely prepared for the elucidation of protein 3D structures by X-ray crystallography, present an ordered and highly accurate 3D array of protein molecules. Inherent to the 3D arrangement of the protein molecules in the crystal is a complementary 3D ...

orbital and the number of H-atoms connected to the central heavy atom (see Table 1). In Figure 1, we of the van der Waals radius of the ith and the jth atoms with values taken from the CHARMM22 force field (seeHAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures Yunqi Li

Careful selection of the best diffraction geometry matched to the sample, with use of high resolution two-dimensional detectors and a mask integration procedure will allow the collection of statistically accurate data for many proteins and crystals with a...

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures for review November 26, 2003) Hydrogen bonding is a key contributor to the exquisite specificity of the interactions within and between biological macromolecules, and hence accurate modeling of such interactions

The burial of hydrophobic amino acids in the protein core is a driving force in protein folding. The extent to which an amino acid interacts with the solvent and the protein core is naturally proportional to the surface area exposed to these environments. However, an accurate calculation of the solvent-accessible ...

Since a protein's dynamic fluctuation inside cells affects the protein's biological properties, we present a novel method to study the ensemble of near-native structures (NNS) of proteins, namely, the conformations that are very similar to the experimentally determined native structure. We show ...

AbstractEfficient and accurate reconstruction of secondary structure elements in the context of protein structure prediction is the major focus of this work. We present a novel approach capable of reconstructing ?-helices and ?-sheets in atomic detail. The method is based on Metropolis Monte Carlo simulations in a ...

Protein-protein docking is the computational prediction of protein complex structure given the individually solved component protein structures. It is an important means for understanding the physicochemical forces that underlie macromolecular interactions and a valuable tool for modeling ...

Abstract. In the wake of the genome data flow, we need- more urgently than ever- accurate tools to predict protein structure. The problem of predicting protein structure from sequence remains fundamentally unsolved despite more than three decades of intensive research effort. However, the ...

Molecular modeling of proteins including homology modeling, structure determination, and knowledge-based protein design requires tools to evaluate and refine three-dimensional protein structures. Steric clash is one of the artifacts prevalent in low-resolution structures ...

We have obtained the (13)C alpha chemical shift tensors for each amino acid in the protein GB1. We then developed a CST force field and incorporated this into the Xplor-NIH structure determination program. GB1 structures obtained by using CST restraints had improved precision over those obtained in the absence of CST restraints and ...

NMR-based structural biology of proteins can be pursued efficiently in supercooled water at temperatures well below the freezing point of water. This enables one to study protein structure, dynamics, hydration and cold denaturation in an unperturbed aqueous solution at very low temperatures. Furthermore, such ...

The Qnr proteins belong to the pentapeptide repeat protein family. Despite each pentapeptide repeat unit being an important structural determinant, accurately determining pentapeptide repeat units in the Qnr proteins through sequence-based alignments has been challenging. In the present study, ...

Identification and characterization of protein functional surfaces are important for predicting protein function, understanding enzyme mechanism, and docking small compounds to proteins. As the rapid speed of accumulation of protein sequence information far exceeds that of structures, ...

for any type of accurate structure determination we need more than this (xray and NMR). #12;Determination the size. #12;2. Gel Filtration Size of a protein determines its rate of passage through a molecular sieve) of a protein is determined by its weight, charge and shape. Charge and shape are standardized for all ...

Accurately predicted protein secondary structure provides useful information for target selection, to analyze protein function and to predict higher dimensional structure. Existing research shows that more data + refined search = better prediction. We analyze relation between the prediction ...

It is currently believed that the atlas of existing protein structures is faithfully represented in the Protein Data Bank. However, whether this atlas covers the full universe of all possible protein structures is still a highly debated issue. By using a sophisticated numerical approach, we ...

It is currently believed that the atlas of existing protein structures is faithfully represented in the Protein Data Bank. However, whether this atlas covers the full universe of all possible protein structures is still a highly debated issue. By using a sophisticated numerical approach, we ...

The side chains of the 20 types of amino acids, owing to a large extent to their different physical properties, have characteristic distributions in interior/surface regions of individual proteins and in interface/non-interface portions of protein surfaces that bind proteins or nucleic acids. These distributions have important ...

Despite recent efforts to develop automated protein structure determination protocols, structural genomics projects are slow in generating fold assignments for complete proteomes, and spatial structures remain unknown for many protein families. Alternative cheap and fast methods to assign folds ...

BackgroundGenome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution structure determination methods make it unlikely that this gap will disappear in the near future. Small angle X-ray scattering (SAXS) is an established low resolution method ...

Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most ...

SummaryThe primary obstacle to de novo protein structure prediction is conformational sampling: the native state generally has lower free energy than non-native structures but is exceedingly difficult to locate. Structure predictions with atomic level accuracy have been made for small proteins ...

The kinetochore is a chromosomally associated structure that is essential for accurate chromosome segregation in mitosis. Kinetochores physically link chromosomes to the spindle but also monitor these interactions through the spindle checkpoint pathway. A...

Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that would accurately describe plant anatomy and morphology. This will facilitate cross-species comparative studies and quantitative comparison of phenotype...

Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that would accurately describe plant anatomy and morphology. This will facilitate cross-species comparative studies and quantitative comparison of phenotyp...

Electron diffraction data and high resolution images can now be used to obtain accurate, three-dimensional density maps of biological macromolecules. These density maps can be interpreted by building an atomic-resolution model of the structure into the ex...

Comparison and classification of folding patterns from a database of protein structures is crucial to understand the principles of protein architecture, evolution and function. Current search methods for proteins with similar folding patterns are slow and computationally intensive. The sharp growth in the number of ...

BackgroundAccurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational ...

Raman spectroscopy measures molecular vibrations triggered by the inelastic scattering of light, while Raman optical activity (ROA) measures a small difference in the Raman scattering from chiral molecules using circularly polarized light. We used Raman or ROA spectra to determine the secondary structure contents (helix, sheet, or other) of proteins. ...

Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various ...

Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various ...

Genetically encoded fluorescent proteins are an essential tool in cell biology, widely used for investigating cellular processes with molecular specificity. Direct uses of fluorescent proteins include studies of the in vivo cellular localization and dynamics of a protein, as well as measurement of its in vivo concentration. In this ...

Three-dimensional structures of only a small fraction of known protein-protein complexes are currently known. Meanwhile, computational methods are of increasing importance to provide structural models for known protein-protein interactions. Current protein-protein docking methods are often ...

Transmembrane ?-barrel (TMB) proteins are embedded in the outer membranes of mitochondria, Gram-negative bacteria, and chloroplasts. These proteins perform critical functions, including active ion-transport and passive nutrient intake. Therefore, there is a need for accurate prediction of secondary and tertiary ...

1 Simple jury predicts protein secondary structure best Burkhard Rost 1,* , Pierre Baldi 2 , Geoff experimented with averaging over the best current methods. The resulting jury decision proved significantly more accurate than the best method. Although the 'jury' seemed the best choice on average, for 60

This paper proposes an efficient ensemble system to tackle the protein secondary structure prediction problem with neural networks as base classifiers. The experimental results show that the multi-layer system can lead to better results. When deploying more accurate classifiers, the higher accuracy of the ensemble system can be ...

Identifying protein binding sites provides important clues to the function of a protein. Experimental methods to identify the binding sites such as determining the crystal structures of protein complexes are extremely laborious and expensive. Here, we present a computational technique called spatial aggregation ...

The efficient and accurate quantification of protein-ligand interactions using computational methods is still a challenging task. Two factors strongly contribute to the failure of docking methods to predict free energies of binding accurately: the insufficient incorporation of protein flexibility coupled to ligand ...

Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous ...

BackgroundWhen accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how ...

BackgroundThe rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB), thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and ...

... THE RELATION OF PROTEIN STRUCTURE TO THE ... ENZYMES, *MOLECULAR STRUCTURE), (*PROTEINS, CATALYSIS), (*CHYMOTRYPSIN ...

Rational drug design relies on the 3D structures of biological macromolecules, with a particular emphasis on proteins. The structural genomics-based high-throughput structure determination platforms established by the Protein Structure Initiative (PSI) of the National ...

The majority of biological processes involve the association of proteins or binding of other ligands to proteins. The accurate prediction of putative binding sites on the protein surface can be very helpful for rational drug design on target proteins of medical relevance, for predicting the ...

BackgroundSearching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioinformatics. While there are many existing methods for structural similarity searching, faster and ...

The Pcons.net Meta Server (http://pcons.net) provides improved automated tools for protein structure prediction and analysis using consensus. It essentially implements all the steps necessary to produce a high quality model of a protein. The whole process is fully automated and a potential user only submits the ...

Proteins are the molecules cells primarily rely on for catalysis, recognition, signaling, defense, locomotion, and structural integrity. Engineering proteins for improved function or new applications is a fast-growing segment of biotechnology and biomedicine. Experimental efforts based on the screening of large mutant libraries have ...

Detection of protein families in large databases is one of the principal research objectives in structural and functional genomics. Protein family classification can significantly contribute to the delineation of functional diversity of homologous proteins, the prediction of function based on domain architecture or ...

X-ray solution scattering in both the small-angle (SAXS) and wide-angle (WAXS) regimes is making an increasing impact on our understanding of biomolecular complexes. The accurate calculation of WAXS patterns from atomic coordinates has positioned the approach for rapid growth and integration with existing Structural Genomics efforts. WAXS data are ...

Membrane proteins are a major product of most genomes and the target of a large number of current pharmaceuticals, yet little information exists on their structures because of the difficulty of crystallising them; hence for the most part they have been excluded from structural genomics programme targets. Furthermore, even methods such ...

Protein structure prediction is a cornerstone of bioinformatics research. Membrane proteins require their own prediction methods due to their intrinsically different composition. A variety of tools exist for topology prediction of membrane proteins, many of them available on the Internet. The server described in ...

As complete genomes accumulate and the generation of genomic biodiversity proceeds at an accelerating pace, the need to understand the interaction between sequence evolution and protein structure and function rises in prominence. The pattern and pace of substitutions in proteins can provide important clues to functional importance, ...

REDCRAFT, a new open source software tool that accommodates the analysis of RDC data for simultaneous structure and dynamics characterization of proteins is presented in this article. Simultaneous consideration of structure and motion is believed to be necessary for accurate representation of the solution-state of ...

REDCRAFT, a new open source software tool that accommodates the analysis of RDC data for simultaneous structure and dynamics characterization of proteins is presented in this article. Simultaneous consideration of structure and motion is believed to be necessary for accurate representation of the solution-state of ...

The prediction of protein structure, based primarily on sequence and structure homology, has become an increasingly important activity. Homology models have become more accurate and their range of applicability has increased. Progress has come, in part, from the flood of sequence and structure ...

SummaryOne of the challenges in protein secondary structure prediction is to overcome the cross-validated 80% prediction accuracy barrier. Here, we propose a novel approach to surpass this barrier. Instead of using a single algorithm that relies on a limited data set for training, we combine two complementary methods having different strengths: Fragment ...

SummaryDiscrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field ...

Careful selection of the best diffraction geometry matched to the sample, with use of high resolution two-dimensional detectors and a mask integration procedure will allow the collection of statistically accurate data for many proteins and crystals with a sample size of at least 1 mm/sup 3/. Accurate data and improved refinement ...

> Featured Programs Protein Structure Initiative Enabling High-Throughput Structural Biology and Structural Genomics Protein Structure Initiative (PSI) The Protein Structure...

BackgroundThe prediction of the secondary structure of a protein is a critical step in the prediction of its tertiary structure and, potentially, its function. Moreover, the backbone dihedral angles, highly correlated with secondary structures, provide crucial information about the local three-dimensional ...

Protein crystals are routinely prepared for the elucidation of protein structure by X-ray crystallography. These crystals present an highly accurate periodical array of protein molecules with accompanying highly ordered porosity made of interconnected voids. The permeability of the porous ...

... Software Pipeline for Protein Structure Prediction. ... sequence similarity to known protein structures. ... SOFTWARE ENGINEERING, *PROTEINS, TEST ...

Since the demonstration that the sequence of a protein encodes its structure, the prediction of structure from sequence remains an outstanding problem that impacts numerous scientific disciplines, including many genome projects. By iteratively fixing secondary structure assignments of residues during Monte Carlo ...

Since demonstrating that a protein's sequence encodes its structure, the prediction of structure from sequence remains an outstanding problem that impacts numerous scientific disciplines including many genome projects. By iteratively fixing secondary structure assignments of residues during Monte Carlo simulations ...

Cysteine residues in proteins are targets of numerous post-translational modifications and play important roles in protein structure and enzymatic function. Consequently, understanding the full biochemistry of proteins depends on determining the oxidation state and availability of the residues to be modified. We ...

We present a method for predicting protein folding class based on global protein chain description and a voting process. Selection of the best descriptors was achieved by a computer-simulated neural network trained on a data base consisting of 83 folding classes. Protein-chain descriptors include overall composition, transition, and ...

Knowledge of protein structures and protein-protein interactions is essential for understanding of biological processes. Recent advances in protein crosslinking and mass spectrometry (MS) have shown significant potential to contribute to this area. Here we report a novel method to rapidly and ...

The dynamic nature of the chromatin fiber provides the structural and functional flexibility required for the accurate transcriptional responses to various stimuli. In living cells, structural proteins such as the linker histone H1 and the High Mobility Group (HMG) proteins continuously ...

... shown to be highly characteristic features of protein structure. ... for structural alignment of proteins and for ... for fragments similar to a chosen structure. ...

Integral membrane protein biogenesis requires the coordination of several events: accurate targeting of the nascent chain to the membrane; recognition, orientation and integration of transmembrane (TM) domains; and proper formation of tertiary and quaternary structure. Initially unanticipated inter- and ...