NMR refinement and peptide folding using the GROMACS software

IF 16.4 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY

Accounts of Chemical Research Pub Date : 2021-03-28 DOI:10.1007/s10858-021-00363-z

Anna Sinelnikova, David van der Spoel

引用次数: 8

Abstract

Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins and nucleic acids. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model distance restraints, dihedral restraints and orientation restraints. The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.

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使用GROMACS软件进行核磁共振细化和肽折叠

核磁共振波谱通常用于研究蛋白质和核酸的三维结构和动力学。结构的确定通常是通过在经典能量函数中加入基于核磁共振数据的约束并进行约束分子模拟来完成的。在这里，我们报告了一个从NMR- star文件中提取NMR约束并将其导出到GROMACS软件的脚本的实现。有了这个软件包，就可以对距离约束、二面体约束和方向约束进行建模。通过执行有约束和没有约束的模拟来验证脚本的输出，包括从头开始细化一个肽。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.