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

Colin Brown, Anuradha Agarwal, View ORCID ProfileAntoni Luque
doi: https://doi.org/10.1101/2023.02.27.529640
Colin Brown
1Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92116, USA
2Department of Physics, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92116, USA
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Anuradha Agarwal
1Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92116, USA
3Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92116, USA
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Antoni Luque
1Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92116, USA
3Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92116, USA
4Deparment of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92116, USA
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  • ORCID record for Antoni Luque
  • For correspondence: aluque@sdsu.edu
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Abstract

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 Statement

The authors have declared no competing interest.

Footnotes

  • http://luquelab.github.io/pyCapsid/

  • https://github.com/luquelab/pyCapsid

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 01, 2023.
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pyCapsid: Identifying dominant dynamics and quasi-rigid mechanical units in protein shells
Colin Brown, Anuradha Agarwal, Antoni Luque
bioRxiv 2023.02.27.529640; doi: https://doi.org/10.1101/2023.02.27.529640
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pyCapsid: Identifying dominant dynamics and quasi-rigid mechanical units in protein shells
Colin Brown, Anuradha Agarwal, Antoni Luque
bioRxiv 2023.02.27.529640; doi: https://doi.org/10.1101/2023.02.27.529640

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