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This article is part of the supplement: Highlights from the 2nd IEEE Symposium on Biological Data Visualization

Open Access Research

Visual cavity analysis in molecular simulations

Julius Parulek1*, Cagatay Turkay1, Nathalie Reuter2 and Ivan Viola13

Author Affiliations

1 Department of Informatics, University of Bergen, Norway

2 CBU, University of Bergen, Norway

3 Vienna University of Technology, Austria

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BMC Bioinformatics 2013, 14(Suppl 19):S4  doi:10.1186/1471-2105-14-S19-S4

Published: 12 November 2013

Abstract

Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel technique, which extracts potential binding sites, represented by cavities, and characterize them by 3D graphs and by amino acids. The binding sites are extracted using an implicit function sampling and graph algorithms. We propose an advanced cavity exploration technique based on the graph parameters and associated amino acids. Additionally, we interactively visualize the graphs in the context of the molecular surface. We apply our method to the analysis of MD simulations of Proteinase 3, where we verify the previously described cavities and suggest a new potential cavity to be studied.