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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Vydané v:PLoS computational biology Ročník 19; číslo 3; s. e1010834
Hlavní autori: Tessmer, Maxx H., Stoll, Stefan
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States Public Library of Science 01.03.2023
Public Library of Science (PLoS)
Predmet:
Analysis
Biology and Life Sciences
Digital Subscriber Line
Electron paramagnetic resonance
Electron paramagnetic resonance spectroscopy
Electron spin
Electron spin resonance
Electron Spin Resonance Spectroscopy
Experiments
Labels
Libraries
Modelling
Models, Molecular
Molecular modelling
Physical Sciences
Proteins
Proteins - chemistry
Python (Programming language)
Research and Analysis Methods
Resonance
Software
Spectroscopy
Spectrum analysis
Spin Labels
Structure
United States
ISSN:1553-7358, 1553-734X, 1553-7358
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Popis
Shrnutí: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.
Bibliografia:new_version
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The authors have declared that there are no competing interests.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1010834