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Open Access Software

KVFinder: steered identification of protein cavities as a PyMOL plugin

Saulo HP Oliveira23, Felipe AN Ferraz12, Rodrigo V Honorato12, José Xavier-Neto1, Tiago JP Sobreira1 and Paulo SL de Oliveira1*

Author Affiliations

1 National Laboratory of Biosciences, P.O. Box 6192, CEP 13083-970 Campinas, SP, Brazil

2 Inter-institutional Grad Program on Bioinformatics, University of São Paulo, Rua do Matão, 1010 IME-USP, Bloco B, sala 137, CEP 05508-050 São Paulo, Brazil

3 System Approaches to Biomedical Sciences Industrial Doctorate Centre - Doctoral Training Centre, University of Oxford, 127, Magdalen Road, Postal code OX4 1RJ Oxford, UK

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BMC Bioinformatics 2014, 15:197  doi:10.1186/1471-2105-15-197

Published: 17 June 2014

Abstract

Background

The characterization of protein binding sites is a major challenge in computational biology. Proteins interact with a wide variety of molecules and understanding of such complex interactions is essential to gain deeper knowledge of protein function. Shape complementarity is known to be important in determining protein-ligand interactions. Furthermore, these protein structural features have been shown to be useful in assisting medicinal chemists during lead discovery and optimization.

Results

We developed KVFinder, a highly versatile and easy-to-use tool for cavity prospection and spatial characterization. KVFinder is a geometry-based method that has an innovative customization of the search space. This feature provides the possibility of cavity segmentation, which alongside with the large set of customizable parameters, allows detailed cavity analyses. Although the main focus of KVFinder is the steered prospection of cavities, we tested it against a benchmark dataset of 198 known drug targets in order to validate our software and compare it with some of the largely accepted methods. Using the one click mode, we performed better than most of the other methods, staying behind only of hybrid prospection methods. When using just one of KVFinder’s customizable features, we were able to outperform all other compared methods. KVFinder is also user friendly, as it is available as a PyMOL plugin, or command-line version.

Conclusion

KVFinder presents novel usability features, granting full customizable and highly detailed cavity prospection on proteins, alongside with a friendly graphical interface. KVFinder is freely available on http://lnbio.cnpem.br/bioinformatics/main/software/ webcite.

Keywords:
KVFinder; Protein cavities; Volume calculation; PyMOL plugin