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

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 ti...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2021-09, Vol.37 (18), p.3038-3040
Main Authors: Rausch, Atilio O, Freiberger, Maria I, Leonetti, Cesar O, Luna, Diego M, Radusky, Leandro G, Wolynes, Peter G, Ferreiro, Diego U, Parra, R Gonzalo
Format: Article
Language:English
Subjects:
Catalytic Domain
Molecular Dynamics Simulation
Proteins
Software
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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. https://github.com/proteinphysiologylab/frustratometeR. Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btab176