From chemistry-request@www.ccl.net Sun Apr 11 00:04:19 1999 Received: from paracelsus.fdm.uni-freiburg.de (paracelsus.fdm.uni-freiburg.de [132.230.97.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id AAA02694 Sun, 11 Apr 1999 00:04:18 -0400 (EDT) Received: (from hubi@localhost) by paracelsus.fdm.uni-freiburg.de (SMI-8.6/8.6.9) id GAA13645; Sun, 11 Apr 1999 06:04:13 +0200 Date: Sun, 11 Apr 1999 06:04:13 +0200 (MET DST) From: "W. Huber" To: chemistry@www.ccl.net Subject: molecular similarity Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am looking for a method, or a software packet, that compares a "drug-like" molecule against a database of other such molecules. The comparison should be based on 3D structure and take into account conformational flexibility of the molecules. Additionally, I would like to use this together with a virtual database, i.e. one that consists of fragments that are assembled according to certain rules. It seems that the combinatorics of all that make compute time be an important issue. I have found a number of references in the literature that offer partial solutions (SEAL, FLEXS, PLM, 3D-MCSS), so I would like to ask: - what is used by practioners in the field, - how they compare against each other (is there a relevant review?), - have I maybe missed the one method that does it all. Best regards... W. Huber hubi@fdm.uni-freiburg.de Freiburg Center for Data Analysis and Modelling Germany