Binding sites and active sites of proteins and DNAs are often associated with structural pockets and cavities. CASTp server uses the weighted Delaunay triangulation and the alpha complex for shape measurements. It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules. It measures analytically the area and volume of each pocket and cavity, both in solvent accessible surface (SA, Richards' surface) and molecular surface (MS, Connolly's surface). It also measures the number of mouth openings, area of the openings, circumference of mouth lips, in both SA and MS surfaces for each pocket.

You can request calculation for a particular molecule. The results will be emailed to you including measured parameters for pockets, cavities and mouth openings, as well as listing of wall atoms and mouth atoms for each pocket. In addition, a RasMol script sent through email will help you to visualization the pocket of your interest.

See http://cast.engr.uic.edu/cast/ or http://sunrise.cbs.umn.edu/cast/