pycapsid
Python package to extract quasi-rigid domains in protein shells and other macromolecular complexes.
Science Score: 59.0%
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○CITATION.cff file
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✓.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
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✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Keywords
Repository
Python package to extract quasi-rigid domains in protein shells and other macromolecular complexes.
Basic Info
- Host: GitHub
- Owner: luquelab
- License: mit
- Language: HTML
- Default Branch: main
- Homepage: https://luquelab.github.io/pyCapsid/
- Size: 114 MB
Statistics
- Stars: 6
- Watchers: 2
- Forks: 1
- Open Issues: 28
- Releases: 5
Topics
Metadata Files
README.md
pyCapsid
Description
pyCapsid is a Python package that identifies dominant motions, rigid domains, and disassembly units of protein shells (and other macromolecular complexes), combining elastic network models and clustering methods. The input of pyCapsid is a molecular structure from the Protein Data Bank (PDBid) or in PDB format. The output of pyCapsid includes a report that includes key analyses and figures.
The quickest way to use pyCapsid is as a Google Colab notebook in the cloud. It only requires a Google account and can analyze from small to medium capsids. For the analysis of larger capsids or high-throughput studies, it is recommended to install pyCapsid from the Python repositories PIP or Conda.
The methodology and application of pyCapsid were recently peer-reviewed and published in Bioinformatics by Oxford Academic: + Brown, Colin, Anuradha Agarwal, and Antoni Luque. "pyCapsid: Identifying dominant dynamics and quasi-rigid mechanical units in protein shells." Bioinformatics, 40(1), btad761, 2024. https://doi.org/10.1093/bioinformatics/btad761
Below, we provide a basic description of the package and repository. We recommend visiting the pyCapsid's online documentation for a more detailed guide to using pyCapsid.
pyCapsid is under an MIT license. If you use pyCapsid on any scientific or scholarly work, please cite the above reference to support this academic and open-source initiative from the Luque lab.
Figure: pyCapsid's key steps. a) The protein shell (atom coordinates, atom types, and B-factors) is inputted using a PDB file (or a PDB ID). (b) The elastic network model (ENM) is calibrated (parametrized). (c) Normal mode analysis (NMA) determines the distance fluctuations between residues. (d) The correlation coefficient of predicted and experimental B-factors is generated for quality control. (e) Spectral clustering is applied to obtain the quasi-rigid molecular domains in the capsid. (f) The fluctuations between residues within the rigid clusters are calculated. (g) The results are mapped back to the capsid protein atomic model for structural interpretation.
Installation
The package requires Python>3.7 and < 3.11; we recommend Python 3.10. Via pip: ~~~~ pip install pyCapsid ~~~~
Via conda: ~~~~ conda install -c luque_lab -c conda-forge pycapsid ~~~~
Documentation
pyCapsid's documentation is available as a GitHub-pages website accessible at https://luquelab.github.io/pyCapsid/. The documentation's source files are located in this repository at https://github.com/luquelab/pyCapsid/tree/main/docs.
Examples and Tutorials
The online Colab notebook contains a default example in the Quick-start guide, which is the simplest way to get started using pyCapsid.
An example of the pyCapsid report is accessible at https://github.com/luquelab/pyCapsid/tree/main/notebooks/pyCapsid_report_example.
The online documentation includes a page with tutorials.
The pyCapsid YouTube playlist includes video tutorials with instructions on using the Colab notebook and visualizing the results in ChimeraX.
Online repositories
pyCapsid is available as a GitHub repository at https://github.com/luquelab/pyCapsid and in Zenodo at the permanent DOI 10.5281/zenodo.8408578.
Project history
This is an evolving repository: + Started: 2022-10-24 + Ended: Ongoing
Folders' description
/conda: Files needed to deploy in Conda's repository./docs: This folder contains the project's documentation./notebooks: Notebooks associated with the project./results: This folder contains the results, performance analysis, and commented references associated with the project./src/pyCapsid: Package's source codes.
Owner
- Name: Luque Lab
- Login: luquelab
- Kind: organization
- Location: San Diego State University
- Website: https://www.luquelab.com
- Repositories: 8
- Profile: https://github.com/luquelab
GitHub Events
Total
- Issues event: 1
- Watch event: 6
- Fork event: 1
Last Year
- Issues event: 1
- Watch event: 6
- Fork event: 1
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 187
- Total Committers: 3
- Avg Commits per committer: 62.333
- Development Distribution Score (DDS): 0.396
Top Committers
| Name | Commits | |
|---|---|---|
| colintravisbrown | 5****n@u****m | 113 |
| Anuradha Agarwal | 9****1@u****m | 56 |
| Antoni Luque | a****e@s****u | 18 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 80
- Total pull requests: 15
- Average time to close issues: 27 days
- Average time to close pull requests: less than a minute
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 0.91
- Average comments per pull request: 0.0
- Merged pull requests: 15
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- luque82 (62)
- colintravisbrown (10)
- abelardoacm (2)
Pull Request Authors
- colintravisbrown (11)
- luque82 (1)
- anuradha1901 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 151 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 56
- Total maintainers: 2
pypi.org: pycapsid
A set of computational tools written in python for the analysis of viral capsids
- Homepage: https://github.com/luquelab/pycapsid
- Documentation: https://pycapsid.readthedocs.io/
- License: MIT License
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Latest release: 0.6.1
published 8 months ago
Rankings
Maintainers (2)
Dependencies
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