From jji at cgl.ucsf.edu Thu Nov 1 10:26:02 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Thu, 01 Nov 2007 10:26:02 -0700 Subject: [Zinc-fans] Stereo isomer In-Reply-To: <731454.18052.qm@web51407.mail.re2.yahoo.com> References: <731454.18052.qm@web51407.mail.re2.yahoo.com> Message-ID: <472A0C2A.7010100@cgl.ucsf.edu> Hi Dzung > > I have a question whether ZINC includes all stereo isomers of a compound? If there are 1 or 2 centers, and the source information is stereochemically ambiguous (e.g. most vendor catalogs), then we attempt to generate all 2 or 4 stereoisomers, respectively. If there are 3 or more ambiguous stereocenters, we attempt to pick the most probable 4, but we're not too confident about this. > For example I am interested in a compound like L-methionine sulfoxide, > and we know this compound has 02 forms L-methionine-S-sulfoxide and L- > methionine-R-sulfoxide. Yes, if L-methionine sulfoxide were in ZINC, and the source catalog were stereo-chemically ambiguous, then both representations should be present. For example Acros Organics compound 22583 is DL-methionine sulfoxide, which is rendered in ZINC as ZINC ID 1529567 and 1666580 . Hope this helps. Happy docking. John From loraine.brillet at cea.fr Wed Nov 7 01:54:06 2007 From: loraine.brillet at cea.fr (BRILLET Loraine 216515) Date: Wed, 7 Nov 2007 10:54:06 +0100 Subject: [Zinc-fans] Zinc ID's of a list of supplier catalog numbers Message-ID: <7E82589CA662294BB063FBCD85928FF9888114@TOKYO.intra.cea.fr> Hi, I have a list of around 16 500 ChemBridge catalog numbers for which I'd like to have their corresponding ZINC ID. How is this possible? (apart of doing it one by one on the ZINC search page...!) Thanks, Loraine _____________________________________________ Loraine Brillet Centre de Criblage pour Macromol?cules Bio-Actives CMBA CEA Grenoble - DSV - iRTSV 17 avenue des Martyrs, 38054 Grenoble cedex 9, France email : loraine.brillet at cea.fr tel : ++33 (0)4 38 78 21 47 fax : ++33 (0)4 38 78 50 32 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20071107/2470e350/attachment.html From jji at cgl.ucsf.edu Wed Nov 7 09:47:43 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Wed, 07 Nov 2007 09:47:43 -0800 Subject: [Zinc-fans] Zinc ID's of a list of supplier catalog numbers In-Reply-To: <7E82589CA662294BB063FBCD85928FF9888114@TOKYO.intra.cea.fr> References: <7E82589CA662294BB063FBCD85928FF9888114@TOKYO.intra.cea.fr> Message-ID: <4731FA3F.1070901@cgl.ucsf.edu> Hi Loraine Thanks for your interest in ZINC, and your question about mapping ChemBridge catalog numbers to ZINC IDs. May I suggest you download the "Purchasing information" for the ChemBridge subset, available from the "by vendors" page under ChemBridge. http://zinc.docking.org/vendor0/chbr/chbr_purch.xls This is a tab-delimited file, which maps ZINC IDs to ChemBridge IDs. Then you just write a 5 line perl or python script to map them. Does this sound ok? Bien ? vous John BRILLET Loraine 216515 wrote: > > Hi, > > > > I have a list of around 16 500 ChemBridge catalog numbers for which > I?d like to have their corresponding ZINC ID. > > How is this possible? (apart of doing it one by one on the ZINC search > page?!) > > > > Thanks, > > > > Loraine > > > > _____________________________________________ > > > > Loraine Brillet > > > > Centre de Criblage pour Macromol?cules Bio-Actives CMBA > > CEA Grenoble - DSV - iRTSV > > > > 17 avenue des Martyrs, 38054 Grenoble cedex 9, France > > email : loraine.brillet at cea.fr > > tel : ++33 (0)4 38 78 21 47 > > fax : ++33 (0)4 38 78 50 32 > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From lhailema at ecn.purdue.edu Mon Nov 12 08:55:28 2007 From: lhailema at ecn.purdue.edu (Leaelaf M Hailemariam) Date: Mon, 12 Nov 2007 11:55:28 -0500 (EST) Subject: [Zinc-fans] Java engine for converting molecular sketches to SMILES strings In-Reply-To: <4731FA3F.1070901@cgl.ucsf.edu> References: <7E82589CA662294BB063FBCD85928FF9888114@TOKYO.intra.cea.fr> <4731FA3F.1070901@cgl.ucsf.edu> Message-ID: Dear Zinc My name is Leaelaf and I am PhD student in Chemical Engineering. I am currently trying to populate a reaction database with SMILES strings. The ZINC search interface has such an engine and I wanted to know if it is available to all and if so how I can get it. regards Leaelaf From jji at cgl.ucsf.edu Tue Nov 13 11:18:09 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Tue, 13 Nov 2007 11:18:09 -0800 Subject: [Zinc-fans] Java engine for converting molecular sketches to SMILES strings In-Reply-To: References: <7E82589CA662294BB063FBCD85928FF9888114@TOKYO.intra.cea.fr> <4731FA3F.1070901@cgl.ucsf.edu> Message-ID: <4739F871.4040309@cgl.ucsf.edu> Hi Leaelaf Thanks for your email, and your interest in ZINC. I am always willing to try to work with people to help them get what they need. Please email me off the list with a little more detail of what you need so we can figure out if I can help you. John Leaelaf M Hailemariam wrote: > Dear Zinc > > My name is Leaelaf and I am PhD student in Chemical Engineering. I am > currently trying to populate a reaction database with SMILES strings. > The ZINC search interface has such an engine and I wanted to know if > it is available to all and if so how I can get it. > > regards > Leaelaf > From emanuele at chemiome.chm.unipg.it Mon Nov 26 00:48:23 2007 From: emanuele at chemiome.chm.unipg.it (emanuele) Date: Mon, 26 Nov 2007 09:48:23 +0100 Subject: [Zinc-fans] Comparison mol2 and smiles files Message-ID: <474A8857.9030909@chemiome.chm.unipg.it> Dear all ZINC-fans, I downloaded the databases Asinex and Sigma-aldrich from the version 7 of ZINC in both the formats SMILES and MOL2. For both the databases I found a difference in the molecules present in the archives, that means some molecules present in the multi-mol2 file and not in the SMILES and vice versa. Is it possible or I did some errors in the comparison? Thanks in advance Regards, Emanuele From jji at cgl.ucsf.edu Mon Nov 26 10:32:03 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Mon, 26 Nov 2007 10:32:03 -0800 Subject: [Zinc-fans] Comparison mol2 and smiles files In-Reply-To: <474A8857.9030909@chemiome.chm.unipg.it> References: <474A8857.9030909@chemiome.chm.unipg.it> Message-ID: <474B1123.4030604@cgl.ucsf.edu> Hi Emanuele Thanks for your email. It is not surprising (to me) if there are a few differences (say 0.1% or so), due to, well, various book keeping problems, some of which we are aware of, but seem to only get corrected asymptotically. If this lack of consistency between mol2 and SMILES is greater than about 0.1%, then a script may have failed. I will take a look and get back to you by tomorrow (Tuesday). John emanuele wrote: > Dear all ZINC-fans, > > I downloaded the databases Asinex and Sigma-aldrich from the version 7 > of ZINC in both the formats SMILES and MOL2. For both the databases I > found a difference in the molecules present in the archives, that means > some molecules present in the multi-mol2 file and not in the SMILES and > vice versa. > > Is it possible or I did some errors in the comparison? > > Thanks in advance > > Regards, > > Emanuele > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans >