FrustratometeR：一个用于计算蛋白质结构、点突变体和分子动力学模拟中局部受挫情况的R包。

FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations.

作者信息

Rausch Atilio O, Freiberger Maria I, Leonetti Cesar O, Luna Diego M, Radusky Leandro G, Wolynes Peter G, Ferreiro Diego U, Parra R Gonzalo

机构信息

Facultad de Ingeniería, Universidad Nacional de Entre Ríos, Entre Ríos E3100XAD, Argentina.

Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.

出版信息

Bioinformatics. 2021 Sep 29;37(18):3038-3040. doi: 10.1093/bioinformatics/btab176.

DOI:10.1093/bioinformatics/btab176

PMID:33720293

Abstract

SUMMARY

Once folded, natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i.e. they are highly frustrated. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein-protein interactions, small ligand recognition, catalytic sites and allostery. Here, we present FrustratometeR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and molecular dynamics (MD) trajectories, allowing straightforward integration of local frustration analysis into pipelines for protein structural analysis.

AVAILABILITY AND IMPLEMENTATION

https://github.com/proteinphysiologylab/frustratometeR.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

天然蛋白质分子一旦折叠，其多肽链内几乎不存在能量冲突。然而，许多蛋白质结构确实包含一些区域，这些区域在折叠后仍存在能量冲突，即它们处于高度受挫状态。这些在进化和生理时间尺度上保持稳定的区域，与天然蛋白质的几个功能方面相关，如蛋白质-蛋白质相互作用、小分子配体识别、催化位点和变构作用。在这里，我们展示了FrustratometeR，一个R包，它可以在个人计算机或集群上轻松计算局部能量受挫情况。这个包有助于对局部受挫、点突变和分子动力学（MD）轨迹进行大规模分析，从而能够将局部受挫分析直接整合到蛋白质结构分析流程中。