PT  - JOURNAL ARTICLE
AU  - Colin Brown
AU  - Anuradha Agarwal
AU  - Antoni Luque
TI  - pyCapsid: Identifying dominant dynamics and quasi-rigid mechanical units in protein shells
AID  - 10.1101/2023.02.27.529640
DP  - 2023 Jan 01
TA  - bioRxiv
PG  - 2023.02.27.529640
4099  - http://biorxiv.org/content/early/2023/03/01/2023.02.27.529640.short
4100  - http://biorxiv.org/content/early/2023/03/01/2023.02.27.529640.full
AB  - pyCapsid 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’s source code is available under MIT License on GitHub (https://github.com/luquelab/pycapsid). It has also been deployed in the 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). In addition, users can post issues regarding pyCapsid in the GitHub repository (https://github.com/luquelab/pyCapsid/issues).Contact Antoni Luque (aluque{at}sdsu.edu).Supplementary information (SI) Further details and figures on the performance results reported in this article are available in the GitHub repository https://github.com/luquelab/pyCapsid/tree/main/results/performance). A gallery displaying the application of pyCapsid to various protein shells is available on the online documentation (https://luquelab.github.io/pyCapsid/gallery/).Competing Interest StatementThe authors have declared no competing interest.