Identification of structurally important amino acids in proteins by graph-theoretic measures
Proceedings of the KDD-09 Workshop on Statistical and Relational Learning in Bioinformatics
| Hi-index | 3.84 |
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. Contact: swanand@cryst.bioc.cam.ac.uk