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chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling

Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular double electron–electron resonance (DEER). It is based on in silico attachment of rotamer ensemble representations of spin labels to protein...

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Detalles Bibliográficos
Autores principales: Tessmer, Maxx H., Stoll, Stefan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10096462/
https://www.ncbi.nlm.nih.gov/pubmed/37000838
http://dx.doi.org/10.1371/journal.pcbi.1010834
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author Tessmer, Maxx H.
Stoll, Stefan
author_facet Tessmer, Maxx H.
Stoll, Stefan
author_sort Tessmer, Maxx H.
collection PubMed
description Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular double electron–electron resonance (DEER). It is based on in silico attachment of rotamer ensemble representations of spin labels to protein structures. chiLife enables the development of custom protein analysis and modeling pipelines using SDSL EPR experimental data. It allows the user to add custom spin labels, scoring functions and spin label modeling methods. chiLife is designed with integration into third-party software in mind, to take advantage of the diverse and rapidly expanding set of molecular modeling tools available with a Python interface. This article describes the main design principles of chiLife and presents a series of examples.
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spelling pubmed-100964622023-04-13 chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling Tessmer, Maxx H. Stoll, Stefan PLoS Comput Biol Research Article Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular double electron–electron resonance (DEER). It is based on in silico attachment of rotamer ensemble representations of spin labels to protein structures. chiLife enables the development of custom protein analysis and modeling pipelines using SDSL EPR experimental data. It allows the user to add custom spin labels, scoring functions and spin label modeling methods. chiLife is designed with integration into third-party software in mind, to take advantage of the diverse and rapidly expanding set of molecular modeling tools available with a Python interface. This article describes the main design principles of chiLife and presents a series of examples. Public Library of Science 2023-03-31 /pmc/articles/PMC10096462/ /pubmed/37000838 http://dx.doi.org/10.1371/journal.pcbi.1010834 Text en © 2023 Tessmer, Stoll https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Tessmer, Maxx H.
Stoll, Stefan
chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling
title chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling
title_full chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling
title_fullStr chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling
title_full_unstemmed chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling
title_short chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling
title_sort chilife: an open-source python package for in silico spin labeling and integrative protein modeling
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10096462/
https://www.ncbi.nlm.nih.gov/pubmed/37000838
http://dx.doi.org/10.1371/journal.pcbi.1010834
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