KVFinder suite

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: an open-source Python package for cavity detection and characterization in biomolecular structures, tailored for data science and automated pipelines.

  • parKVFinder: an open-source software designed to detect and comprehensively characterize biomolecular cavities of any type, integrated with a PyMOL plugin.

  • KVFinder-web: an open-source web-based application for cavity detection and characterization in biomolecular structures.

Scientific team

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), Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM)

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.

Citing pyKVFinder

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.

Issues

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

On Issues page, you can file a:

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!

Funding

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).

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.