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KVFinder suite
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The **KVFinder suite** is a set of tools for cavity detection and characterization in biomolecular structures, including but not limited to proteins and nucleic acids. It is composed of the following components:

* `pyKVFinder <https://github.com/LBC-LNBio/pyKVFinder/>`_: an open-source Python package for cavity detection and characterization in biomolecular structures, tailored for data science and automated pipelines.
* `parKVFinder <https://github.com/LBC-LNBio/parKVFinder/>`_: an open-source software designed to detect and comprehensively characterize biomolecular cavities of any type, integrated with a PyMOL plugin.
* `KVFinder-web <https://kvfinder-web.cnpem.br>`_: an open-source web-based application for cavity detection and characterization in biomolecular structures.

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Scientific team
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pyKVFinder and PyMOL pyKVFinder Tools were developed by:

* João V. S. Guerra
* 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

Computational Biology Laboratory (`LBC <https://github.com/LBC-LNBio>`_), Brazilian Biosciences National Laboratory (`LNBio <https://lnbio.cnpem.br/>`_), Brazilian Center for Research in Energy and Materials (`CNPEM <https://cnpem.br>`_)

If you have any further questions, inquires or if you wish to contribute to KVFinder project, please contact us at joao.guerra@lnbio.cnpem.br or paulo.oliveira@lnbio.cnpem.br.

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Citing pyKVFinder
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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.

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Issues
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pyKVFinder package uses GitHub for project management. Please help us by reporting any problems or requests.

On `Issues <https://github.com/LBC-LNBio/pyKVFinder/issues>`_ page, you can file a:

.. toctree::
    
    Bug Report <https://github.com/LBC-LNBio/pyKVFinder/issues/new?assignees=&labels=&projects=&template=bug_report.yml&title=%5BBug%5D%3A+>
    Documentation <https://github.com/LBC-LNBio/pyKVFinder/issues/new?assignees=&labels=documentation&projects=&template=documentation.yml&title=%5BDoc%5D%3A+>
    Feature Request <https://github.com/LBC-LNBio/pyKVFinder/issues/new?assignees=&labels=enhancement&projects=&template=feature_request.yml&title=%5BENH%5D%3A+>
    Maintenance <https://github.com/LBC-LNBio/pyKVFinder/issues/new?assignees=&labels=enhancement&projects=&template=maintenance.yml&title=%5BMNT%5D%3A+>


Only make sure the bug or request has not already been reported. Click on “Search” and enter some keywords to search.

Thank you for helping us improve pyKVFinder!

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Funding
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This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [Grant Number 350244/2020-0], Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES) [Grant Number 88887.928702/2023-00], and Brazilian Center for Research in Energy and Materials (CNPEM).

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License
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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.