FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations
| Autor: | R. Gonzalo Parra, Atilio O Rausch, Peter G. Wolynes, Diego M. Luna, Leandro G Radusky, Maria I. Freiberger, Diego U. Ferreiro, Cesar O. Leonetti |
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| Rok vydání: | 2020 |
| Předmět: |
Statistics and Probability
Physics 0303 health sciences media_common.quotation_subject Mutant 030302 biochemistry & molecular biology Frustration Biochemistry Computer Science Applications Folding (chemistry) 03 medical and health sciences Computational Mathematics R package Molecular dynamics Protein structure Computational Theory and Mathematics Personal computer Cluster (physics) Point (geometry) Statistical physics Molecular Biology 030304 developmental biology media_common |
| Zdroj: | Bioinformatics (Oxford, England). |
| ISSN: | 1367-4811 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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