Voronoia

Calculating packing densities of proteins and ligands

Voronoia is a program suite to analyse and visualize the atomic packing of protein structures. It is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. Voronoia is also targeted to detect locations of putative internal water or binding sites for ligands. Accordingly, Voronoia is beneficial for a broad range of protein structure approaches. It is applicable as a standalone version coming with a user friendly GUI or, alternatively, as a Pymol Plugin. Finally, Voronoia is also available as an easy to use webtool to process user defined PDB-files or to asses precalculated packing files from DOPP, the regularly updated Dictionary of Packing in Proteins.

When using Voronoia, please cite:
Rother K, Hildebrand PW, Goede A, Gruening B, Preissner R.
Voronoia: analyzing packing in protein structures.
Nucleic Acids Res. 2009 Jan;37(Database issue):D393-5.