Voro3D: 3D Voronoi tessellations applied to protein structures.
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.


BACKGROUND
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


BACKGROUND
franck.dupuis@sanofi-aventis.com; jean-paul-mornon@imcp.jussieu.fr.
Dupuis
Franck
F
Laboratoire de Minéralogie Cristallographie Paris, CNRS UMR 7590 Universités Paris 6 et 7, case 115, 4 Place Jussieu, 75252 Paris, France. franck.dupuis@sanofi-aventis.com
Sadoc
Jean-François
JF
Jullien
Rémi
R
Angelov
Borislav
B
Mornon
Jean-Paul
JP
D000465:Algorithms; D000595:Amino Acid Sequence; D003196:Computer Graphics; D003198:Computer Simulation; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013329:Structure-Activity Relationship; D014584:User-Computer Interface
D011506:Proteins