On Apr 27, 2009, at 11:46 AM, Angel Herráez wrote: > Vincent Le Guilloux wrote: > >> And just a question for my curiosity: in the feature list of the cdk >> is indicated " active site detection " in protein structures. Could >> you tell me a few words about that ? Just what (existing?) algorithm >> do you use, and if there is a publication :) > > I cannot imagine that a general algorithm can exist for that. How > would you define an active site? > Maybe it refers to sites defined in the pdb file, which are amino > acid residues identified as such by the authors. > There is a token keyword for that in pdb format, called SITE if I > recollect correctly. > Current Jmol version recognizes such records.
Well the CDK has a pocket finder - which is obviously not specific to active sites, but in conjunction with other methods could be used to identify them http://pele.farmbio.uu.se/nightly/api/org/openscience/cdk/protein/ProteinPocketFinder.html ------------------------------------------------------------------- Rajarshi Guha <rg...@indiana.edu> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Q: What's polite and works for the phone company? A: A deferential operator. ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensign option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
