Format

Send to

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2005 Aug 1;21(15):3316-7. Epub 2005 Jun 2.

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.

Author information

1
Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK. swanand@cryst.bioc.cam.ac.uk

Abstract

SUMMARY:

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.

AVAILABILITY:

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.

PMID:
15932902
DOI:
10.1093/bioinformatics/bti523
[Indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems
    Loading ...
    Support Center