Development of a scoring method for predicting protein complex structures

Abstract

The information about protein-protein interactions increases much more rapidly than the increase of the number of the tertiary structures of those protein complexes. Therefore, precise prediction of protein complex structures by protein-protein docking simulations is required. When the protein complex is rebuilt from its component protomers which derive from experimentally determined complex structure (native structure) by docking, the complex models with rmsd < 10 A from the native structure (near-native model) could be obtained, along with a great number of false positives (decoy). The separation of near-native models from many decoys is therefore needed in the prediction of complex structures by docking. In this study, we developed the method for scoring docking models so that the near-native models were higher in rank than decoys, based on the assumption that the interfaces of near-native models are more complementary in terms of surface properties and shapes compared to those of decoys.