Protein–Protein Binding Sites Prediction by 3D Structural Similarities

Identifying the location of binding sites on proteins is of fundamental importance for a wide range of applications including molecular docking, de novo drug design, structure identification, and comparison of functional sites. In this paper, we develop an efficient approach for finding binding sites between proteins. Our approach consists of four steps: local sequence alignment, protein surface detection, 3D structure comparison, and candidate binding site selection. A comparison of our method with the LSA algorithm shows that the binding sites predicted by our method are somewhat closer to the actual binding sites in the protein-protein complexes. The software package is available at http://sites.google.com/site/guofeics/pro-bs for noncommercial use.