Computing the Protein Binding Sites

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. Structural genomic projects are beginning to produce protein structures with unknown functions. Therefore, efficient methods are required if all these structures are to be properly annotated. When comparing a complete protein with all complete protein structures in the PDB database, experiments show that all the existing approaches have recall values less than 50%. This implies that more than 50% of real binding sites cannot be reported by those existing approaches. We develop an efficient approach for finding binding sites between two proteins. Our approach consists of three steps, local sequence alignment, protein surface detection, and 3D structures comparison. Experiments show that the average recall value of our approach is 82% and the precision of our approach is also significantly better than the existing approaches. The software package is available at http://sites.google.com/site/guofeics/bsfinder.