PocketMatch is a software for comparison of binding sites in a frame invariant manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites.
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Kalidas Yeturu and Nagasuma Chandra(2008)
PocketMatch: A new algorithm to compare binding sites in protein structures
BMC Bioinformatics 2008, 9:543