Refining near-native protein-protein docking decoys by local resampling and energy minimization.

ABSTRACT: How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in

SUBMITTER: Liang S 

PROVIDER: S-EPMC3867632 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature