DockRank: ranking docked conformations using partner-specific sequence homology-based protein interface prediction.

ABSTRACT: Selecting near-native conformations from the immense number of conformations generated by docking programs remains a major challenge in molecular docking. We introduce DockRank, a novel approach to scoring docked conformations based on the degree to which the interface residues of the docked conformation match a set of predicted interface residues. DockRank uses interface residues predicted by partner-specific sequence homology-based protein-protein interface predictor (PS-HomPPI), which predicts the interface residues of a query protein with a specific interaction partner. We compared the performance of DockRank with several state-of-the-art docking scoring functions using Success Rate (the percentage of cases that have at least one near-native conformation among the top m conformations)

SUBMITTER: Xue LC 

PROVIDER: S-EPMC4417613 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature