3D Voronoï tessellations applied to protein structures

Voro3D is an original tool which provides a brand new point of view on protein 3D structures. In order to perform a 3D Voronoï tessellation, 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, 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 or to quantify the contact areas between a protein and a ligand, for instance.

Voro3D user's guide

An example of Voro3D screen :

Starting from any PDB file, Voro3D allows to :

• Select the points representing amino acids (alpha carbons, geometric centers)
  
• Embed your protein structure in a model environment made of a relaxed random packing of spheres
  Choose the sphere radius as well as the number of environment layers
  Relax this environment as many times as you want
  
• Perform the Voronoi tessellation or the Laguerre polyhedral decomposition (weighted Voronoi tessellation). In the latter case it is possible to choose different weights
• Visualize the structure and its environment
• Visualize the tessellation superimposed on the protein structure, modify several graphic parameters 
• Derive all the values concerning the cells and the cell faces
• Assign automatically the secondary structure elements according to the VoTAP procedure
  Derive environment accessibility and contact matrices
• Export the visualization files (*.wrl) to internet or to your PowerPoint presentations thanks to the VRML viewer
  

More information ? See these articles :

• Soyer, A., Chomilier, J., Mornon J.P., Jullien, R. and Sadoc, J.F. (2000). Voronoi tessellation reveals the condensed matter character of folded proteins. Phys Rev Lett, 85, 3532-3535.
• Angelov, B., Sadoc, J.F., Jullien, R., Soyer, A., Mornon, J.P. and Chomilier, J. (2002). Nonatomic solvent-driven Voronoi tessellation of proteins : an open tool to analyse protein folds. Proteins, 49, 446-456.
• Sadoc, J.F., Jullien, R. and Rivier, N. (2003). The Laguerre polyhedral decomposition : application to protein folds. Eur. Phys. J. B., 33, 355-363.
• Dupuis, F., Sadoc, J.F. and Mornon, J.P. (2004). Protein secondary structure assignment through Voronoi tessellation. Proteins, 55, 519-528
  

To install this programm on your PC (windows 98, 2000, NT, XP) :

• download the file voro3Dsetup.zip   (or here)
• uncompress it
• double click on Setup.exe
• then double click on cortvrml.exe

Voro3D was designed by Franck Dupuis in collaboration with :

• Jean-Paul Mornon, Laboratoire de Minéralogie Cristallographie Paris, Equipe de Biologie Structurale, Université Paris 6 et 7, France
• Jean-François Sadoc, Laboratoire de Physique des Solides, Université Paris 11, Orsay, France
• Rémi Jullien, Laboratoire des Verres, Université de Montpellier 2, Montpellier, France
• Borislav Angelov Institute of Biophysics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, Sofia 1113, Bulgaria