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

Swanand P. Gore; David F. Burke; Tom L. Blundell

doi:10.1093/bioinformatics/bti523

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

Swanand P. Gore^*, David F. Burke, Tom L. Blundell

^*Corresponding author for this work

Centre for Host Microbiome Interactions

Cambridge University Hospitals NHS Foundation Trust

Research output: Contribution to journal › Article › peer-review

17 Citations (Scopus)

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.

Original language	English
Pages (from-to)	3316-3317
Number of pages	2
Journal	Bioinformatics
Volume	21
Issue number	15
DOIs	https://doi.org/10.1093/bioinformatics/bti523
Publication status	Published - 1 Aug 2005

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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.",

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

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