Paul Ashford, David S. Moss, Alexander Alex, Siew K. Yeap, Alice Povia, Irene Nobeli & Mark A. Williams(2012). Visualisation of variable binding pockets on protein surfaces by probabalistic analysis of related structure sets. Submitted


Probabalistic analysis of pocket variation

"Provar" (Probability of variation) is a method for probabalistic scoring of pocket predictions across large sets of related protein structures. These scores are the overall probabilities of particular atoms or residues being found to be lining a pocket in the set of structures. Scores output in PDB format files can be readily visualized through simple colour-coding atoms or residues. The approach can help compare pockets across multiple conformations of a protein such as those generated by tCONCOORD or any other simulation method. By supplying a suitable sequence alignment it is also possible to visualize pocket conservation across a set of homologous structures. We enable the input of results from several pocket programs, which allows for comparison between those programs.


The software is written as a series of Matlab modules controlled from a single user-modifiable configuration file. It requires only a base Matlab v7+ installation and the Statistics Toolbox to function. The software can be downloaded here. In dowloading the software you agree to be bound by the terms of the Creative Commons licence under which it is released.

The manual is also included as part of the download.