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.
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Guo, F., Li, S.C., Wang, L. (2012). P-Binder: A System for the Protein-Protein Binding Sites Identification. In: Bleris, L., Măndoiu, I., Schwartz, R., Wang, J. (eds) Bioinformatics Research and Applications. ISBRA 2012. Lecture Notes in Computer Science(), vol 7292. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30191-9_13
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DOI: https://doi.org/10.1007/978-3-642-30191-9_13
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