Protein-protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring

Protein protein docking has made much progress in recent years, but challenges still exist. Here we present the application of our docking approach Ho Dock in CAPRI. In this approach, a binding site prediction is implemented to reduce docking sampling space and filter out unreasonable docked structures, and a network-based enhanced combinatorial scoring function HPNCscore is used to evaluate the decoys. The experimental information was combined with the predicted binding site to pick out the most likely key binding site residues. We applied the Ho Dock method in the recent rounds of the CAPRI experiments, and got good results as predictors on targets 39, 40, and 41. We also got good results as scorers on targets 35, 37, 40, and 41. This indicates that our docking approach can contribute to the progress of protein protein docking methods and to the understanding of the mechanism of protein protein interactions. Proteins 2010; 78:3150-3155. (C) 2010 Wiley-Liss, Inc.