Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles

被引：73

作者：

Mirjalili, Vahid ^{[1
,2
]}

Feig, Michael ^{[1
,3
]}

机构：

[1] Michigan State Univ, Dept Biochem & Mol Biol, E Lansing, MI 48824 USA

[2] Michigan State Univ, Dept Mech Engn, E Lansing, MI 48824 USA

[3] Michigan State Univ, Dept Chem, E Lansing, MI 48824 USA

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2013年 / 9卷 / 02期

基金：

美国国家科学基金会;

关键词：

HIGH-RESOLUTION REFINEMENT; STRUCTURE PREDICTION; HOMOLOGY MODELS; ENERGY; SIMULATIONS; CONFORMATIONS; BOTTLENECKS; POTENTIALS; SEGMENTS; PROGRESS;

D O I：

10.1021/ct300962x

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

A molecular dynamics (MD) simulation based protocol for structure refinement of template-based model predictions is described. The protocol involves the application of restraints, ensemble averaging of selected subsets, interpolation between initial and refined structures, and assessment of refinement success. It is found that submicro-second MD-based sampling when combined with ensemble averaging can produce moderate but consistent refinement for most systems in the CASP targets considered here.

引用

收藏

页码：1294 / 1303

页数：10

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