PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.
CONCLUSIONS
Voronoi tessellation has proved to be a useful tool in protein structure analysis. We have developed PROVAT, a versatile public domain software that enables computation and visualization of Voronoi tessellations of proteins and protein complexes. It is a set of Python scripts that integrate freely available specialized software (Qhull, Pymol etc.) into a pipeline. The calculation component of the tool computes Voronoi tessellation of a given protein system in a way described by a user-supplied XML recipe and stores resulting neighbourhood information as text files with various styles. The Python pickle file generated in the process is used by the visualization component, a Pymol plug-in, that offers a GUI to explore the tessellation visually.


BACKGROUND
PROVAT source code can be downloaded from http://raven.bioc.cam.ac.uk/~swanand/Provat1, which also provides a webserver for its calculation component, documentation and examples.
Gore
Swanand P
SP
Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK. swanand@cryst.bioc.cam.ac.uk
Burke
David F
DF
Blundell
Tom L
TL
D000465:Algorithms; D001665:Binding Sites; D003196:Computer Graphics; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D011506:Proteins