On the use of distance constraints in protein-protein docking computations

Protein–protein docking (PPD) is a computational process that predicts the structure of a complex of two interacting proteins from their unbound structures. The accuracy of PPD predictions is low, but can be greatly enhanced if experimentally determined distance data are available for incorporation...

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Bibliographic Details
Published in:Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2012-01, Vol.80 (1), p.194-205
Main Authors: Shih, Edward S. C., Hwang, Ming-Jing
Format: Article
Language:English
Subjects:
Algorithms
CAPRI
complex structure prediction
Computer Simulation
DPPD
Magnetic Resonance Spectroscopy
Models, Molecular
Multiprotein Complexes - chemistry
Protein Binding
Protein Interaction Domains and Motifs
Protein Structure, Quaternary
Protein Structure, Tertiary
protein-protein interaction
ZDOCK
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Summary:Protein–protein docking (PPD) is a computational process that predicts the structure of a complex of two interacting proteins from their unbound structures. The accuracy of PPD predictions is low, but can be greatly enhanced if experimentally determined distance data are available for incorporation into the prediction. However, the specific effects of distance constraints on PPD predictions are largely uncharacterized. In this study, we systematically simulated the effects of using distance constraints both on a new distance constraint‐driven PPD approach, called DPPD, and also, by re‐ranking, on a well‐established grid‐based global search approach. Our results for a PPD benchmark dataset of 84 protein complexes of known structures showed that near 100% docking success rates could be obtained when the number of distance constraints exceeded six, the degrees of freedom of the system, but the success rate was significantly reduced by long distance constraints, large binding‐induced conformational changes, and large errors in the distance data. Our results also showed that, under most conditions simulated, even two or three distance constraints were sufficient to achieve a much better success rate than those using a sophisticated physicochemical function to re‐rank the results of the global search. Our study provides guidelines for the practical incorporation of experimental distance data to aid PPD predictions. Proteins 2012;. © 2011 Wiley Periodicals, Inc.
ISSN:0887-3585
1097-0134
DOI:10.1002/prot.23179