chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling.
Maxx H TessmerStefan StollPublished in: PLoS computational biology (2023)
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.
Keyphrases
- room temperature
- single molecule
- density functional theory
- transition metal
- protein protein
- molecular docking
- high resolution
- amino acid
- binding protein
- molecular dynamics
- energy transfer
- big data
- data analysis
- electronic health record
- artificial intelligence
- mass spectrometry
- solar cells
- neural network
- deep learning
- electron microscopy
- electron transfer