Acta Phys. -Chim. Sin. ›› 2012, Vol. 28 ›› Issue (11): 2729-2734.doi: 10.3866/PKU.WHXB201208162

• BIOPHYSICAL CHEMISTRY • Previous Articles     Next Articles

Division of Protein Surface Patches and Its Application in Protein Binding Site Prediction

WANG Pan-Wen1, GONG Xin-Qi2, LI Chun-Hua1, CHEN Wei-Zu1, WANG Cun-Xin1   

  1. 1 College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China;
    2 School of Life Sciences, Tsinghua University, Beijing 100084, P. R. China
  • Received:2012-05-25 Revised:2012-08-16 Published:2012-10-17
  • Contact: LI Chun-Hua, WANG Cun-Xin;
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (31171267, 10974008), Beijing Natural Science Foundation, China (4102006), International Science & Technology Cooperation Program of China (2010DFA31710), and Fundamental Research Fund for the Beijing Municipal Education Commission Science and Technology Innovation Platform, China.


Binding site prediction for protein-protein complexes is a challenging problem in the area of computational molecular biology. Using a set of double-chain complexes in Benchmark 3.0, we calculated the solvent accessible surface areas and inter-residue contact areas for each monomer and propose a division method of protein surface patches. We found that the products of the solvent accessible surface areas and internal contact areas of patches, the PSAIA values, could provide protein binding site information. In a dataset of 78 complexes, either receptors or ligands of 74 complexes had interface patches with the first or second greatest PSAIA values among all surface patches. A good docking result was achieved when the binding site information obtained with this method was applied in Target 39 of the CAPRI experiment. This patch-based protein binding site prediction method differs from traditional methods, which are based on single residue and consider only surface residues. This provides a new method for binding site prediction in protein-protein interactions.

Key words: Protein binding site prediction, Patch division, Solvent accessible surface area, Interior contact area


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