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PrefMD：一个通过分子动力学模拟进行蛋白质结构精修的网络服务器。

PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

机构信息

Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.

出版信息

Bioinformatics. 2018 Mar 15;34(6):1063-1065. doi: 10.1093/bioinformatics/btx726.

DOI:10.1093/bioinformatics/btx726
PMID:29126101
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5860225/
Abstract

SUMMARY: Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. AVAILABILITY AND IMPLEMENTATION: PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git. CONTACT: feig@msu.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

摘要

摘要：蛋白质结构模型的精修是结构生物信息学中长期存在的问题。基于分子动力学的方法已成为实现一致精修的途径。PREFMD 网络服务器实现了一种基于在 CASP11 中成功测试的方法的优化方案。使用最近的 CASP 精修靶标进行验证表明，与其他最先进的服务器相比，该方法在全局结构准确性方面具有更一致和更显著的改进。

可用性和实现：PREFMD 作为一个网络服务器，可在 http://feiglab.org/prefmd 上免费获得。作为独立软件包运行 PREFMD 的脚本可在 https://github.com/feiglab/prefmd.git 上获得。

联系人：feig@msu.edu。

补充信息：补充数据可在“Bioinformatics”在线获得。

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本文引用的文献

[1]
Computational protein structure refinement: Almost there, yet still so far to go.

Wiley Interdiscip Rev Comput Mol Sci. 2017

[2]
CHARMM36m: an improved force field for folded and intrinsically disordered proteins.

Nat Methods. 2017-1

[3]
Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.

J Chem Inf Model. 2016-7-25

[4]
Assessment of refinement of template-based models in CASP11.

Proteins. 2016-9

[5]
Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade.

Proteins. 2016-9

[6]
Template based protein structure modeling by global optimization in CASP11.

Proteins. 2016-9

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

Proteins. 2016-9

[8]
Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines.

Proteins. 2014-5

[9]
Evaluation of predictions in the CASP10 model refinement category.

Proteins. 2014-2

[10]
GalaxyRefine: Protein structure refinement driven by side-chain repacking.

Nucleic Acids Res. 2013-6-3

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