fpocket

fpocket is a very fast open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program. A GUI is in development and mdpocket (fpocket on md trajectories) is out now. fpocket includes two other programs (dpocket & tpocket) that allow you to extract pocket descriptors and test own scoring functions respectively. Furthermore a nifty druggability prediction score has been added to fpocket recently.
As the algorithm is very fast it can be used on a large scale level (PDB size for instance).