A Graph-Based Approach for Protein-Protein Docking

Protein-protein docking is the computational approach to predict protein-protein interactions. The 3D geometric matching plays an important role in docking because a good matching between proteins provides a good cue for searching the interactional interfaces between them. In this paper, we propose a graph-based approach to search for the protein binding site. Given two proteins, we first identify the cavities in one protein based on the a shape theory. Then we bind the two proteins together by partial matching the cavities with the local shape of another protein. The partial shape matching problem is converted to that of detecting the maximum clique in graph theory. By solving it, we are able to compute the best rigid transformation for docking. The proposed approach has been applied to the docking experiments of IGFBP4 and IGF1 under different circumstances, and the results demonstrate the reliability of our approach.