Protein structure refinement via molecular-dynamics simulations: What works and what does not?

被引：50

作者：

Feig, Michael ^{[1
,2
]}

Mirjalili, Vahid ^{[1
,3
]}

机构：

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

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

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

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2016年 / 84卷

关键词：

CASP; structure prediction; scoring; protein; Molprobity; STRUCTURE PREDICTION; ENERGY MINIMIZATION; STRUCTURE SELECTION; FORCE-FIELD; MODELS; POTENTIALS; CASP10; CONFORMATIONS;

D O I：

10.1002/prot.24871

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Protein structure refinement during CASP11 by the Feig group was described. Molecular dynamics simulations were used in combination with an improved selection and averaging protocol. On average, modest refinement was achieved with some targets improved significantly. Analysis of the CASP submission from our group focused on refinement success versus amount of sampling, refinement of different secondary structure elements and whether refinement varied as a function of which group provided initial models. The refinement of local stereochemical features was examined via the MolProbity score and an updated protocol was developed that can generate high-quality structures with very low MolProbity scores for most starting structures with modest computational effort. (C) 2015 Wiley Periodicals, Inc.

引用

页码：282 / 292

页数：11

共 37 条

[1] Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles [J].