Citation: WANG Pan-Wen, NG Xin-Qi, LI Chun-Hua, CHEN Wei-Zu, WANG Cun-Xin. Division of Protein Surface Patches and Its Application in Protein Binding Site Prediction[J]. Acta Physico-Chimica Sinica doi: 10.3866/PKU.WHXB201208162 shu

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

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 Date: 25 May 2012
Available Online: 16 August 2012
Fund Project: 国家自然科学基金(31171267, 10974008) (31171267, 10974008) 北京市自然科学基金(4102006) (4102006) 科技部国际合作项目(2010DFA31710) (2010DFA31710)

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 od 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.
- Protein binding site prediction,
- Patch division,
- Solvent accessible surface area,
- Interior contact area
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