pyFoldX: enabling biomolecular analysis and engineering along structural ensembles

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• dc.contributor.author Radusky, Leandro
• dc.contributor.author Serrano Pubull, Luis, 1982-
• dc.date.accessioned 2022-04-05T10:07:21Z
• dc.date.available 2022-04-05T10:07:21Z
• dc.date.issued 2022
• dc.description.abstract Recent years have seen an increase in the number of structures available, not only for new proteins but also for the same protein crystallized with different molecules and proteins. While protein design software have proven to be successful in designing and modifying proteins, they can also be overly sensitive to small conformational differences between structures of the same protein. To cope with this, we introduce here pyFoldX, a python library that allows the integrative analysis of structures of the same protein using FoldX, an established forcefield and modeling software. The library offers new functionalities for handling different structures of the same protein, an improved molecular parametrization module, and an easy integration with the data analysis ecosystem of the python programming language. pyFoldX rely on the FoldX software for energy calculations and modelling, which can be downloaded upon registration in http://foldxsuite.crg.eu/ and its licence is free of charge for academics. The pyFoldX library is open-source. Full details on installation, tutorials covering the library functionality, and the scripts used to generate the data and figures presented in this paper are available at https://github.com/leandroradusky/pyFoldX.
• dc.description.sponsorship This work was supported by funds from the European Regional Development Fund (ERDF) and the Generalitat de Catalunya [VEIS-001-P-001647, Programa Operatiu FEDER de Catalunya 2014-2020] and funds from Spanish Ministry of Science, Innovation and University (MCIU) [PGC2018-101271-B-I00]. The authors also acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the Centres de Recerca de Catalunya (CERCA) Programme/Generalitat de Catalunya
• dc.format.mimetype application/pdf
• dc.identifier.citation Radusky LG, Serrano L. pyFoldX: enabling biomolecular analysis and engineering along structural ensembles. Bioinformatics. 2022;38(8):2353-5. DOI: 10.1093/bioinformatics/btac072
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btac072
• dc.identifier.issn 1367-4811
• dc.identifier.uri http://hdl.handle.net/10230/52827
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Bioinformatics. 2022;38(8):2353-5.
• dc.rights © Leandro G. Radusky, Luis Serrano 2022. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial Licens (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.other Biologia molecular
• dc.subject.other Proteïnes
• dc.subject.other Programari
• dc.title pyFoldX: enabling biomolecular analysis and engineering along structural ensembles
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion