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.
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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.
BMC Bioinformatics. 2012 Mar 14;13:39.