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Nucleic Acids Research Advance Access published online on October 23, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn769
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Voronoia: analyzing packing in protein structures

Kristian Rother1,*, Peter Werner Hildebrand2, Andrean Goede3, Bjoern Gruening4 and Robert Preissner4

1International Institute for Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warszawa, Poland, 2Institut for Medical Physics and Biophysics, Charité - University Medicine Berlin, Ziegelstr. 5-9, 10098 Berlin, 3Institute for Biochemistry, Charité - University Medicine Berlin, Monbijoustrasse 2, 10117 Berlin and 4Institute of Molecular Biology and Bioinformatics, Charité - University Medicine Berlin, Arnimallee 22, 14195 Berlin, Germany

*To whom correspondence should be addressed. Tel: +48 60 70 95 012; Fax: +48 22 597 07 15; Email: krother{at}genesilico.pl

Received August 15, 2008. Revised October 6, 2008. Accepted October 7, 2008.

The packing of protein atoms is an indicator for their stability and functionality, and applied in determining thermostability, in protein design, ligand binding and to identify flexible regions in proteins. Here, we present Voronoia, a database of atomic-scale packing data for protein 3D structures. It is based on an improved Voronoi Cell algorithm using hyperboloid interfaces to construct atomic volumes, and to resolve solvent-accessible and -inaccessible regions of atoms. The database contains atomic volumes, local packing densities and interior cavities calculated for 61 318 biological units from the PDB. A report for each structure summarizes the packing by residue and atom types, and lists the environment of interior cavities. The packing data are compared to a nonredundant set of structures from SCOP superfamilies. Both packing densities and cavities can be visualized in the 3D structures by the Jmol plugin. Additionally, PDB files can be submitted to the Voronoia server for calculation. This service performs calculations for most full-atomic protein structures within a few minutes. For batch jobs, a standalone version of the program with an optional PyMOL plugin is available for download. The database can be freely accessed at: http://bioinformatics.charite.de/voronoia.


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