Using residue propensities and tightness of fit to improve rigid-body protein-protein docking

Abstract

Protein-protein interactions are fundamental as many proteins mediate their biological function through protein interactions. Over the past 20 years there have been many computational approaches to dock proteins. These approaches are mostly based on the shape complementarity of structures and the physio-chemical properties of the interfaces. However, these docking approaches are far from perfect and there still remains potential space to improve. We propose to use family-based residue interaction propensity as well as the tightness of fit between residues with high propensities as a scoring function to improve rigid body docking. This approach is evaluated on an established benchmark data set. Our scoring function improves the number of hits for enzyme-inhibitor complexes by a factor of 4-30 in comparison with shape complementarity alone and for antibodyantigen complexes by 4-11. The supplementary data are available at http://www.biotec.tu-dresden. de/\~bhuang/bdock.