Voro3d: 3d Voronoi tessellations applied to protein structures

Bioinformatics Advance Access published June 24, 2004 Summary: Voro3D is an original easy-to-use tool which provides a brand new point of view on protein structures through the 3D Voronoi tessellations. In order to construct the Voronoi cells associated to each amino acid by a number of different tessellation methods, 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, 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 under windows 98, 2000, NT, XP can be freely downloaded a