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Updated: Aug 23, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Voro3D: 3D Voronoi tessellations applied to protein structures
Franck Dupuis1, Jean-François Sadoc, Rémi Jullien
1Laboratoire 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
Unlabelled:
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@sanofi-aventis.com; jean-paul-mornon@imcp.jussieu.fr.
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