From owner-chemistry@ccl.net Thu Jul 19 12:49:00 2007 From: "Michael K Gilson gilson_+_umbi.umd.edu" To: CCL Subject: CCL: Full Download of BindingDB's Protein-Ligand Affinity Data Message-Id: <-34763-070719124537-2695-+s+y/j2eyLYMuUnn4QJaeA,server.ccl.net> X-Original-From: "Michael K Gilson" Date: Thu, 19 Jul 2007 12:45:29 -0400 Sent to CCL by: "Michael K Gilson" [gilson-*-umbi.umd.edu] Dear Colleagues, BindingDB now allows downloading of all ~16,000 compounds in the form of an SDfile, which includes affinities for the protein targets and selected additional information, such as relevant PDB IDs: http://www.bindingdb.org/bind/chemsearch/marvin/PolicyNotice.jsp?all_download=yes Molecules are available with 2D coordinates or computed 3D coordinates. The files are ~100 MB in size. We do ask that you register and agree not to redistribute the data commercially. Please be patient if you encounter some initial glitches, as the download service is new and relatively untested. Feel free to contact me with comments and questions. I hope you find the data useful! Best regards, Mike -- Michael K. Gilson, M.D., Ph.D. CARB Fellow and Professor Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville, MD 20850 Voice: 240-314-6217 Fax: 240-314-6255 gilsonumbi.umd.edu Lab Page: gilsonlab.umbi.umd.edu BindingDB: www.bindingdb.org From owner-chemistry@ccl.net Thu Jul 19 16:15:00 2007 From: "Igor Filippov Contr igorf%a%helix.nih.gov" To: CCL Subject: CCL: OSRA: Optical Structure Recognition Message-Id: <-34764-070719160050-18504-HaamKafta64er9bmmaUKig]-[server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 19 Jul 2007 15:16:38 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf%a%helix.nih.gov] Dear Colleagues, We would like to announce a new addition to the set of chemoinformatics tools available from the Computer-Aided Drug Design Group at the NCI-Frederick. OSRA is a utility designed to convert graphical representations of chemical structures, such as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick (GIF, JPEG, PNG, TIFF, PDF, PS etc.) and generate the SMILES representation of the molecular structure images encountered within that document. You are welcome to download the free standalone version of the software at http://cactus.nci.nih.gov/osra/ or try our web-based interface to OSRA available at http://cactus.nci.nih.gov/cgi-bin/osra/index.cgi Comments, criticisms, contribution of ideas and participation in further development of OSRA are most welcome. Igor Filippov, Marc Nicklaus ------------------------------------------------------------------------ CADD Group NIH/NCI at Frederick E-mail addresses: Bldg 376 igorf(0)helix.nih.gov 376 Boyles Street mn1(0)helix.nih.gov FREDERICK, MD 21702 USA Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://ccr.cancer.gov/Staff/Staff.asp?profileid=6282 ------------------------------------------------------------------------ From owner-chemistry@ccl.net Thu Jul 19 19:11:00 2007 From: "Karen.Green]![sanofi-aventis.com" To: CCL Subject: CCL: similar to CLiDE? RE: OSRA: Optical Structure Recognition Message-Id: <-34765-070719190858-32311-5cY3l86rit5A2Rgsg74OWQ|a|server.ccl.net> X-Original-From: content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Jul 2007 16:08:12 -0700 MIME-Version: 1.0 Sent to CCL by: [Karen.Green:+:sanofi-aventis.com] Hi, Igor, This sounds like a free version of batch-mode/full version of CLiDE [http://www.simbiosys.ca/clide/]... Karen --- Karen M. Green, Ph.D. Karen.Green^sanofi-aventis.com Research Investigator Drug Design Group -----Original Message----- > From: owner-chemistry^ccl.net [mailto:owner-chemistry^ccl.net] Sent: Thursday, July 19, 2007 12:17 PM To: Green, Karen M. PH/US Subject: CCL: OSRA: Optical Structure Recognition Sent to CCL by: "Igor Filippov [Contr]" [igorf%a%helix.nih.gov] Dear Colleagues, We would like to announce a new addition to the set of chemoinformatics tools available from the Computer-Aided Drug Design Group at the NCI-Frederick. OSRA is a utility designed to convert graphical representations of chemical structures, such as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick (GIF, JPEG, PNG, TIFF, PDF, PS etc.) and generate the SMILES representation of the molecular structure images encountered within that document. You are welcome to download the free standalone version of the software at http://cactus.nci.nih.gov/osra/ or try our web-based interface to OSRA available at http://cactus.nci.nih.gov/cgi-bin/osra/index.cgi Comments, criticisms, contribution of ideas and participation in further development of OSRA are most welcome. Igor Filippov, Marc Nicklaus ------------------------------------------------------------------------ CADD Group NIH/NCI at Frederick E-mail addresses: Bldg 376 igorf]![helix.nih.gov 376 Boyles Street mn1]![helix.nih.gov FREDERICK, MD 21702 USA Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://ccr.cancer.gov/Staff/Staff.asp?profileid=6282 ------------------------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt