Ranking Docked Models of Protein-Protein Complexes Using Predicted Partner-Specific Protein-Protein Interfaces: A Preliminary Study.

ABSTRACT: Computational protein-protein docking is a valuable tool for determining the conformation of complexes formed by interacting proteins. Selecting near-native conformations from the large number of possible models generated by docking software presents a significant challenge in practice. We introduce a novel method for ranking docked conformations based on the degree of overlap between the interface residues of a docked conformation formed by a pair of proteins with the set of predicted interface residues between them. Our approach relies on a method, called PS-HomPPI, for reliably predicting protein-protein interface residues by taking into account information derived from both interacting proteins. PS-HomPPI infers the residues of a query protein that are likely to interact with a partner

SUBMITTER: Xue LC 

PROVIDER: S-EPMC4403796 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature