Python package to detect and characterize cavities in biomolecular structures

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  • License Expression: GPL-3.0-or-later
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  • Author: Helder V. Ribeiro-Filho, Luiz F. G. Alves, Pablo W. A. Silva, Gabriel E. Jara, Leandro O. Bortot, José G. C. Pereira, Paulo S. Lopes-de-Oliveira
  • Tags structural biology , proteins , biomolecules , cavity detection , cavity characterization , binding sites
  • Requires: Python >=3.10
  • Provides-Extra: dev , docs , plugins
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Project description

pyKVFinder

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A Python package for detecting and characterizing biomolecular cavities.

See also:

Installation

To install the latest release on PyPI, run:

pip install pyKVFinder

Or to install the latest developmental version, run:

git clone https://github.com/LBC-LNBio/pyKVFinder.git
pip install -e pyKVFinder

Citation

If you use pyKVFinder package, please cite:

Guerra, J. V. S., Ribeiro-Filho, H. V., Jara, G. E., Bortot, L. O., Pereira, J. G. C., & Lopes-de-Oliveira, P. S. (2021). pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. BMC bioinformatics, 22(1), 607. https://doi.org/10.1186/s12859-021-04519-4.

If you use pyKVFinder.Molecule, please also cite:

Guerra, J. V. S., Alves, L. F. G., Bourissou, D., Lopes-de-Oliveira, P. S., & Szalóki, G. (2023). Cavity Characterization in Supramolecular Cages. Journal of chemical information and modeling, 63(12), 3772-3785. https://doi.org/10.1021/acs.jcim.3c00328.

If you use PyMOL pyKVFinder Tools, please also cite:

Guerra, J. V. da S., Ribeiro Filho, H. V., Bortot, L. O., Honorato, R. V., Pereira, J. G. de C., & Lopes-de-Oliveira, P. S. (2020). ParKVFinder: A thread-level parallel approach in biomolecular cavity detection. In SoftwareX (Vol. 12, p. 100606). Elsevier BV. https://doi.org/10.1016/j.softx.2020.100606.

License

The software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Project details

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  • License Expression: GPL-3.0-or-later
    SPDX License Expression
  • Author: Helder V. Ribeiro-Filho, Luiz F. G. Alves, Pablo W. A. Silva, Gabriel E. Jara, Leandro O. Bortot, José G. C. Pereira, Paulo S. Lopes-de-Oliveira
  • Tags structural biology , proteins , biomolecules , cavity detection , cavity characterization , binding sites
  • Requires: Python >=3.10
  • Provides-Extra: dev , docs , plugins
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