P-Binder: a system for the protein-protein binding sites identification

Authors:
Fei Guo;Shuai Cheng Li;Lusheng Wang
Affiliations:
School of Computer Science and Technology, Shandong University, Jinan, Shandong, China,Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong;Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong;Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
Venue:
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Year:
2012

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Abstract

Determination of binding sites between proteins has a wide range of applications. Understanding energetics and mechanism of complexes remains one of the essential problems in binding site prediction. We develop a system, P-Binder, for identifying binding sites based on structural compatibility, side-chain conformations, amino acid types and contact energies. P-Binder utilizes an enumeration method and side-chain packing program to identify structurally compatible sites. The system reports the sites with the highest ranked configurations, evaluated through a combination of four statistical energy items. We test P-Binder on protein-protein docking Benchmark v4.0. The overall accuracy and coverage are 64.0% and 69.4% for the bound state, and 51.1% and 61.4% for the unbound state. A comparison with some existing techniques shows P-Binder to improve the success rate by at least 12.3%. The system reports improvements in prediction quality, in terms of both accuracy and coverage. The software package is available at http://sites.google.com/site/guofeics/p-binder for non-commercial use.