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Bioinformatics Advance Access originally published online on June 24, 2004
Bioinformatics 2005 21(8):1715-1716; doi:10.1093/bioinformatics/bth365
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Voro3D: 3D Voronoi tessellations applied to protein structures

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

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

*To whom correspondence should be addressed.

Summary: Voro3D is an original easy-to-use tool, which provides a brand new point of view on protein structures through the three-dimensional (3D) Voronoi tessellations. To construct the Voronoi cells associated with each amino acid by a number of different tessellation methods, Voro3D uses a protein structure file in the PDB format as an input. After calculation, different structural properties of interest like secondary structures assignment, environment accessibility and 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 using Windows 98, 2000, NT, XP can be freely downloaded at http://www.lmcp.jussieu.fr/~mornon/voronoi.html

Contact: franck.dupuis{at}sanofi-aventis.com; jean-paul-mornon{at}imcp.jussieu.fr


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