Voro3D: 3D Voronoi tessellations applied to protein structures

Bioinformatics
Franck DupuisJean-Paul Mornon

Abstract

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. 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 franck.dupuis@sanofi-aventis.com; jean-paul-mornon@imcp.jussieu.fr.

References

Oct 13, 2000·Physical Review Letters·A SoyerJ F Sadoc
Apr 20, 2004·Current Opinion in Structural Biology·Anne Poupon
Apr 23, 2004·Proteins·Franck DupuisJean-Paul Mornon

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Citations

Sep 25, 2008·Quarterly Reviews of Biophysics·Joël JaninPinak Chakrabarti
Jun 4, 2005·Bioinformatics·Swanand P GoreTom L Blundell
Oct 25, 2008·Nucleic Acids Research·Kristian RotherRobert Preissner
Nov 18, 2005·The European Physical Journal. E, Soft Matter·J F Sadoc
Aug 25, 2011·BMC Bioinformatics·Joan SeguraNarcis Fernandez-Fuentes
Nov 10, 2013·Bioinformatics·Lydia BenkaidaliMichel Petitjean
Jun 17, 2009·Protein Science : a Publication of the Protein Society·Evandro Ferrada, Francisco Melo
Jul 17, 2009·Protein Science : a Publication of the Protein Society·Manoj TyagiAlexandre G de Brevern
Sep 8, 2010·Proteins·Canan AtilganAli Rana Atilgan
Apr 6, 2006·Transfusion clinique et biologique : journal de la Société française de transfusion sanguine·I CallebautJ-P Cartron
Aug 28, 2016·Journal of Molecular Modeling·Mathieu FossépréDaniel P Vercauteren
Jan 1, 2008·Bioinformatics and Biology Insights·Guillaume FourtyJean-Paul Mornon
Dec 21, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M Ferraro, L Zaninetti

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