An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.

ABSTRACT: Structure prediction on a genomic scale requires a simplified energy function that can efficiently sample the conformational space of polypeptide chains. A good energy function at minimum should discriminate native structures against decoys. Here, we show that a recently developed, residue-specific, all-atom knowledge-based potential (167 atomic types) based on distance-scaled, finite ideal-gas reference state (DFIRE-all-atom) can be substantially simplified to 20 residue types located at side-chain center of mass (DFIRE-SCM) without a significant change in its capability of structure discrimination. Using 96 standard multiple decoy sets, we show that there is only a small reduction (from 80% to 78%) in success rate of ranking native structures as the top 1. The success rate is higher than

SUBMITTER: Zhang C 

PROVIDER: S-EPMC2286718 | biostudies-literature | 2004 Feb

REPOSITORIES: biostudies-literature