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An accurate, residue‐level, pair potential of mean force for folding and binding based on the distance‐scaled, ideal‐gas reference state
Author(s) -
Zhang Chi,
Liu Song,
Zhou Hongyi,
Zhou Yaoqi
Publication year - 2004
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.03348304
Subject(s) - decoy , statistical potential , chemistry , native state , crystallography , protein structure , biological system , protein structure prediction , biochemistry , receptor , biology
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 two previously developed, all‐atom distance‐dependent statistical pair potentials. Applied to structure selections of 21 docking decoys without modification, the DFIRE‐SCM potential is 29% more successful in recognizing native complex structures than an all‐atom statistical potential trained by a database of dimeric interfaces. The potential also achieves 92% accuracy in distinguishing true dimeric interfaces from artificial crystal interfaces. In addition, the DFIRE potential with the C α positions as the interaction centers recognizes 123 native structures out of a comprehensive 125‐protein TOUCHSTONE decoy set in which each protein has 24,000 decoys with only C α positions. Furthermore, the performance by DFIRE‐SCM on newly established 25 monomeric and 31 docking Rosetta‐decoy sets is comparable to (or better than in the case of monomeric decoy sets) that of a recently developed, all‐atom Rosetta energy function enhanced with an orientation‐dependent hydrogen bonding potential.