NDLI: Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Kozakov, Dima Hall, David R. Beglov, Dmitri Brenke, Ryan Comeau, Stephen R. Shen, Yang Li, Keyong Zheng, Jiefu Vakili, Pirooz Paschalidis, Ioannis Ch Vajda, Sandor
Description	Country affiliation: United States Author Affiliation: Kozakov D ( BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts 02215, USA. vajda@bu.edu)
Abstract	Our approach to protein-protein docking includes three main steps. First, we run PIPER, a rigid body docking program based on the Fast Fourier Transform (FFT) correlation approach, extended to use pairwise interactions potentials. Second, the 1000 best energy conformations are clustered, and the 30 largest clusters are retained for refinement. Third, the stability of the clusters is analyzed by short Monte Carlo simulations, and the structures are refined by the medium-range optimization method SDU. The first two steps of this approach are implemented in the ClusPro 2.0 protein-protein docking server. Despite being fully automated, the last step is computationally too expensive to be included in the server. When comparing the models obtained in CAPRI rounds 13-19 by ClusPro, by the refinement of the ClusPro predictions and by all predictor groups, we arrived at three conclusions. First, for the first time in the CAPRI history, our automated ClusPro server was able to compete with the best human predictor groups. Second, selecting the top ranked models, our current protocol reliably generates high-quality structures of protein-protein complexes from the structures of separately crystallized proteins, even in the absence of biological information, provided that there is limited backbone conformational change. Third, despite occasional successes, homology modeling requires further improvement to achieve reliable docking results.
File Format	HTM / HTML
ISSN	08873585
e-ISSN	10970134
DOI	10.1002/prot.22835
Journal	Proteins: Structure, Function, and Bioinformatics
Issue Number	15
Volume Number	78
Language	English
Publisher	Wiley-Liss
Publisher Date	2010-11-15
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Research Support, N.i.h., Extramural Research Support, U.s. Gov't, Non-p.h.s. Models, Chemical Protein Multimerization Computational Biology Discipline Biochemistry Metabolism Molecular Dynamics Simulation Proteins Chemistry Algorithms Protein Binding Protein Conformation Monte Carlo Method Cluster Analysis
Content Type	Text
Resource Type	Article
Subject	Structural Biology Biochemistry Molecular Biology

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Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19

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Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19.

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Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19

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Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19.