pyCapsid: Identifying dominant dynamics and quasi-rigid mechanical units in protein shells

Abstract

Structured AbstractO_ST_ABSSummaryC_ST_ABSpyCapsid is a Python package developed to facilitate the characterization of the dynamics and mechanical units of protein shells and other protein complexes. The package was developed in response to the rapid increase of high-resolution structures, particularly capsids of viruses, requiring multiscale biophysical analyses. Given a protein shell, pyCapsid generates the collective vibrations of its amino-acid residues, identifies quasi-rigid mechanical regions, and maps the results back to the input proteins for interpretation. pyCapsid summarizes the main results in a report that includes publication-quality figures. Availability and ImplementationpyCapsids source code is available under MIT License on GitHub (https://github.com/luquelab/pycapsid). It is compatible with Python 3.8-3.10 and has been deployed in two leading Python package-management systems, PIP (https://pypi.org/project/pyCapsid/) and Conda (https://anaconda.org/luque_lab/pycapsid). Installation instructions and tutorials are available in the GitHub Page-style online documentation (https://luquelab.github.io/pyCapsid). Additionally, a cloud-based implementation of pyCapsid is available as a Google Colab notebook (https://colab.research.google.com/github/luquelab/pyCapsid/blob/main/notebooks/pyCapsid_colab_notebook.ipynb). pyCapsid Colab does not require installation and generates the same report and outputs as the installable version. Users can post issues regarding pyCapsid in the GitHub repository (https://github.com/luquelab/pyCapsid/issues).