This software is developed by Kalidas (http://openwetware.org/wiki/Kalidas_Y) as part of his Ph.D. thesis. The method enables alignment of ligand molecules considered molecular graphs. It is useful in the domain of drug discovery and bioinformatics.
PocketDepth helps determine binding grooves for protein molecules. Applicable in Bioinformatics and Drug discovery. Literature - http://www.ncbi.nlm.nih.gov/pubmed/17949996 Author's thesis - http://openwetware.org/wiki/Kalidas_Y