From chemistry-request&$at$&ccl.net Sun Nov 2 11:30:25 2003 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA2GTrhP003504 for ; Sun, 2 Nov 2003 11:29:53 -0500 Received: (from mn1 ^at^ localhost) by helix.nih.gov (8.11.7-8.359.2.8/8.11.6) id hA2GTpt39572300; Sun, 2 Nov 2003 11:29:51 -0500 (EST) Date: Sun, 2 Nov 2003 11:29:51 -0500 From: "M. Nicklaus" To: Donald Keidel cc: chemistry{at}ccl.net, "M. Nicklaus" Subject: CCL:Program to search SD/MDL formatted files from chemical companies In-Reply-To: <000101c39cf7$81cc2240$529c178a -8 at 8- dopetec> Message-ID: References: <000101c39cf7$81cc2240$529c178a #at# dopetec> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Don, The chemoinformatics toolkit CACTVS has very powerful substructure search capabilities. It is free for academic use. See http://www2.ccc.uni-erlangen.de/software/cactvs/. We have, e.g., based our online Enhanced NCI Database Browser (http://cactus.nci.nih.gov/ncidb2/) on it. We are using CACTVS to search in SD files numbering in the millions of compounds (although you get a huge additional speedup if you first convert them into the internal CACTVS format). We are working to put a more complete CACTVS documentation together - if you are interested, feel free to contact me. For all other questions, please contact the author of CACTVS, Wolf-Dietrich Ihlenfeldt (wdi{at}xemistry.com). Cheers, Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1{at}helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design Group Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------ On Mon, 27 Oct 2003, Donald Keidel wrote: > Hello, > > I am looking for a program to search SD/MDL formatted files (chemical > company libraries of compounds). I have found ISIS/Base and 3DFS, but I > was wondering if anyone knows of others that might be cheaper than > ISIS/Base (hopefully free), but commercial examples would be of great > help also. Thank you in advance to anyone who reads and responds to > this request. Have a great day. > > Don > > ------------------------------------------------------------------------ > --------------------------------------- > Donald J. Keidel > University of California, Riverside > Department of Biochemistry and Molecular Biology > Riverside, CA 92521 > phone: (909) 787-5493 > fax: (909) 787-4434 > dopetec{at}dslextreme.com > webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm