期刊
JOURNAL OF MOLECULAR BIOLOGY
卷 427, 期 15, 页码 2562-2576出版社
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2015.05.022
关键词
knowledge-based potential; inter-residue contact; contact orientation and distance; icosahedrons; finite ideal gas reference state
资金
- National Science Foundation [1066471]
- Direct For Computer & Info Scie & Enginr
- Division of Computing and Communication Foundations [1066471] Funding Source: National Science Foundation
The relative distance and orientation in contacting residue pairs plays a significant role in protein folding and stabilization. We hereby devise a new knowledge-based, coarse-grained contact potential, so-called ICOSA, by correlating inter-residue contact distance and orientation in evaluating pair-wise inter-residue interactions. The rationale of our approach is to establish icosahedral local coordinates to estimate the statistical residue contact distributions in all spherical triangular shells within a sphere. We extend the theory of finite ideal gas reference state to icosahedral local coordinates. ICOSA incorporates long-range contact interactions, which is critical to ICOSA sensitivity and is justified in statistical rigor. With only backbone atoms information, ICOSA is at least comparable to all-atom, fine-grained potentials such as Rosetta, DFIRE, I-TASSER, and OPUS in discriminating near-natives from misfold protein conformations in the Rosetta and I-TASSER protein decoy sets. ICOSA also outperforms a set of widely used coarse-grained potentials and is comparable to all-atom, fine-grained potentials in identifying CASP10 models. (C) 2015 Elsevier Ltd. All rights reserved.
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