The PocketFEATURE algorithm seeks similar microenvironments within two binding sites, and assesses overall binding site similarity by the presence of multiple shared microenvironments.

Both the original perl implementation (http://simtk.org/home/pocketfeature) and the newer python implementation (http://simtk.org/home/pocketfeature2) produce text-based alignment results, with some small differences between implementations. FEATURE-Viz provides a web-based interface to visualize and manipulate alignments.