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Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

1 , 2 , 1 , *


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      Computational prediction of the 3D structures of molecular interactions is a challenging area, often requiring significant computational resources to produce structural predictions with atomic-level accuracy. This can be particularly burdensome when modeling large sets of interactions, macromolecular assemblies, or interactions between flexible proteins. We previously developed a protein docking program, ZDOCK, which uses a fast Fourier transform to perform a 3D search of the spatial degrees of freedom between two molecules. By utilizing a pairwise statistical potential in the ZDOCK scoring function, there were notable gains in docking accuracy over previous versions, but this improvement in accuracy came at a substantial computational cost. In this study, we incorporated a recently developed 3D convolution library into ZDOCK, and additionally modified ZDOCK to dynamically orient the input proteins for more efficient convolution. These modifications resulted in an average of over 8.5-fold improvement in running time when tested on 176 cases in a newly released protein docking benchmark, as well as substantially less memory usage, with no loss in docking accuracy. We also applied these improvements to a previous version of ZDOCK that uses a simpler non-pairwise atomic potential, yielding an average speed improvement of over 5-fold on the docking benchmark, while maintaining predictive success. This permits the utilization of ZDOCK for more intensive tasks such as docking flexible molecules and modeling of interactomes, and can be run more readily by those with limited computational resources.

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      Most cited references 25

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      The Protein Data Bank.

      The Protein Data Bank (PDB; ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
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        ZDOCK: an initial-stage protein-docking algorithm.

        The development of scoring functions is of great importance to protein docking. Here we present a new scoring function for the initial stage of unbound docking. It combines our recently developed pairwise shape complementarity with desolvation and electrostatics. We compare this scoring function with three other functions on a large benchmark of 49 nonredundant test cases and show its superior performance, especially for the antibody-antigen category of test cases. For 44 test cases (90% of the benchmark), we can retain at least one near-native structure within the top 2000 predictions at the 6 degrees rotational sampling density, with an average of 52 near-native structures per test case. The remaining five difficult test cases can be explained by a combination of poor binding affinity, large backbone conformational changes, and our algorithm's strong tendency for identifying large concave binding pockets. All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at rong/dock. Copyright 2003 Wiley-Liss, Inc.
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          Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

          A geometric recognition algorithm was developed to identify molecular surface complementarity. It is based on a purely geometric approach and takes advantage of techniques applied in the field of pattern recognition. The algorithm involves an automated procedure including (i) a digital representation of the molecules (derived from atomic coordinates) by three-dimensional discrete functions that distinguishes between the surface and the interior; (ii) the calculation, using Fourier transformation, of a correlation function that assesses the degree of molecular surface overlap and penetration upon relative shifts of the molecules in three dimensions; and (iii) a scan of the relative orientations of the molecules in three dimensions. The algorithm provides a list of correlation values indicating the extent of geometric match between the surfaces of the molecules; each of these values is associated with six numbers describing the relative position (translation and rotation) of the molecules. The procedure is thus equivalent to a six-dimensional search but much faster by design, and the computation time is only moderately dependent on molecular size. The procedure was tested and validated by using five known complexes for which the correct relative position of the molecules in the respective adducts was successfully predicted. The molecular pairs were deoxyhemoglobin and methemoglobin, tRNA synthetase-tyrosinyl adenylate, aspartic proteinase-peptide inhibitor, and trypsin-trypsin inhibitor. A more realistic test was performed with the last two pairs by using the structures of uncomplexed aspartic proteinase and trypsin inhibitor, respectively. The results are indicative of the extent of conformational changes in the molecules tolerated by the algorithm.

            Author and article information

            [1 ]Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
            [2 ]Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
            Koç University, Turkey
            Author notes

            Conceived and designed the experiments: BGP YH ZW. Performed the experiments: BGP. Analyzed the data: BGP. Contributed reagents/materials/analysis tools: YH. Wrote the paper: BGP ZW.

            Role: Editor
            PLoS One
            PLoS ONE
            Public Library of Science (San Francisco, USA )
            19 September 2011
            : 6
            : 9
            Pierce et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
            Pages: 6
            Research Article
            Protein Structure
            Biophysics Simulations
            Macromolecular Assemblies
            Computational Biology
            Macromolecular Structure Analysis
            Macromolecular Complex Analysis
            Biochemical Simulations
            Protein Interactions
            Computer Science
            Computerized Simulations
            Software Engineering



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