KVFinder: steered identification of protein cavities as a PyMOL plugin

Author(s)

Oliveira, Saulo H. P. ^{[1, 2]} ; Ferraz, Felipe A. N. ^{[3, 1]} ; Honorato, Rodrigo V. ^{[3, 1]} ; Xavier-Neto, Jose ^[3] ; Sobreira, Tiago J. P. ^[3] ; de Oliveira, Paulo S. L. ^[3]

Affiliation

^[1] Univ Sao Paulo, Interinst Grad Program Bioinformat, BR-05508050 Sao Paulo - Brazil

^[2] Univ Oxford, Doctoral Training Ctr, Syst Approaches Biomed Sci Ind Doctorate Ctr, Oxford OX4 1RJ - England

^[3] Natl Lab Biosci, BR-13083970 Campinas, SP - Brazil

• Document type: Journal article
• Source: BMC Bioinformatics; v. 15, JUN 17 2014.
• Web of Science Citations: 48

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/. (AU)

• FAPESP's process: 09/06433-0 - Development of an algorithm to identify and characterize cavities in specific regions of three-dimensional structures of proteins.
• Grantee: Saulo Henrique Pires de Oliveira
• Support Opportunities: Scholarships in Brazil - Master