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Bioinformatics Advance Access published online on June 24, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth365
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 7, 2004
Revised June 3, 2004
Accepted June 9, 2004

Applications note

Voro3D: 3D voronoi tessellations applied to protein structures

Franck Dupuis 1*, Jean-François Sadoc 2, Rémi Jullien 3, Borislav Angelov 2, Jean-Paul Mornon 1

1 Laboratoire de Minéralogie Cristallographie Paris, CNRS UMR 7590 Universités Paris 6 et 7, case 115, 4 Place Jussieu, 75252 Paris, France
2 Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris 11, Orsay, France
3 Laboratoire des Verres, CNRS UMR 5587, Université Montpellier 2, Montpellier, France

* To whom correspondence should be addressed. E-mail: franck.dupuis{at}lmcp.jussieu.fr.


  Abstract

Summary: Voro3D is an original easy-to-use tool which provides a brand new point of view on protein structures through the 3D Voronoi tessellations. In order to construct the Voronoi cells associated to each amino acid by a number of different tessellation methods, Voro3D uses as input a protein structure file in the PDB format. After calculation, different structural properties of interest like secondary structures assignment, environment accessibility, exact contact matrices can be derived without any geometrical cut-off. Voro3D provides also a visualization of these tessellations superimposed on the associated protein structure, from which it is possible to model a polygonal protein surface using a model solvent or to quantify, for instance, the contact areas between a protein and a ligand.

Availability: the software executable file for PC under windows 98, 2000, NT, XP can be freely downloaded at http://www.lmcp.jussieu.fr/~mornon/voronoi.html.


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