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Bioinformatics Advance Access originally published online on June 2, 2005
Bioinformatics 2005 21(15):3316-3317; doi:10.1093/bioinformatics/bti523
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes

Swanand P. Gore *, David F. Burke and Tom L. Blundell

Department of Biochemistry, University of Cambridge 80 Tennis Court Road, Cambridge, CB2 1GA, UK

*To whom correspondence should be addressed.

Summary: Voronoi tessellation has proved to be a useful tool in protein structure analysis. We have developed PROVAT, a versatile public domain software that enables computation and visualization of Voronoi tessellations of proteins and protein complexes. It is a set of Python scripts that integrate freely available specialized software (Qhull, Pymol etc.) into a pipeline. The calculation component of the tool computes Voronoi tessellation of a given protein system in a way described by a user-supplied XML recipe and stores resulting neighbourhood information as text files with various styles. The Python pickle file generated in the process is used by the visualization component, a Pymol plug-in, that offers a GUI to explore the tessellation visually.

Availability: PROVAT source code can be downloaded from http://raven.bioc.cam.ac.uk/~swanand/Provat1, which also provides a webserver for its calculation component, documentation and examples.

Contact: swanand{at}cryst.bioc.cam.ac.uk

Received on April 19, 2005; revised on May 28, 2005; accepted on May 29, 2005

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