From bkokiopo.MathStat.CPES.uoguelph@msnet.mathstat.uoguelph.ca Wed Jul 22 07:52:11 1998 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA03594 Wed, 22 Jul 1998 07:52:10 -0400 (EDT) Received: from msnet.mathstat.uoguelph.ca (msnet.mathstat.uoguelph.ca [131.104.32.59]) by ccshst09.cs.uoguelph.ca (8.8.6/8.8.6) with ESMTP id HAA21393 for ; Wed, 22 Jul 1998 07:52:11 -0400 (EDT) Received: from MSNET/SpoolDir by msnet.mathstat.uoguelph.ca (Mercury 1.40); 22 Jul 98 07:49:59 -0500 Received: from SpoolDir by MSNET (Mercury 1.40); 22 Jul 98 07:49:57 -0500 From: "Bill Kokiopoulos" To: chemistry@www.ccl.net Date: Wed, 22 Jul 1998 07:49:53 -500 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: CAS RN-SMILES database/software? Priority: normal X-mailer: Pegasus Mail v3.40 (NDS) Message-ID: <17F0D1642DC@msnet.mathstat.uoguelph.ca> Hi my question are: Is there any kind of database (ASCII file) or software from which I can get SMILES representations of compounds as an output by providing the corresponding CAS Registry Numbers as an input? If there exist such databases /software please let me know which are they and how I can get them (maybe give me a URL I can check out). Many Thanks Vassilios (Bill) Kokiopoulos University of Guelph e-mail : bkokiopo@msnet.mathstat.uoguelph.ca From wdi@lesath.organik.uni-erlangen.de Wed Jul 22 09:58:01 1998 Received: from faui45.informatik.uni-erlangen.de (root@faui45.informatik.uni-erlangen.de [131.188.2.45]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA05808 Wed, 22 Jul 1998 09:57:59 -0400 (EDT) Received: from mail2.organik.uni-erlangen.de (lesath.organik.uni-erlangen.de [131.188.128.10]) by faui45.informatik.uni-erlangen.de (8.9.1/8.1.41-FAU) with ESMTP id PAA07215 for ; Wed, 22 Jul 1998 15:57:49 +0200 (MET DST) Received: from wtewael.organik.uni-erlangen.de (wtewael [131.188.128.216]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id PAA14171; Wed, 22 Jul 1998 15:53:37 +0200 (MET DST) Received: (from wdi@localhost) by wtewael.organik.uni-erlangen.de (8.8.7/8.1.59-FAU) id NAA23367; Wed, 22 Jul 1998 13:52:10 GMT From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9807221552.ZM23365@torvs.ccc.uni-erlangen.de> Date: Wed, 22 Jul 1998 15:52:09 -0600 In-Reply-To: "Bill Kokiopoulos" "CCL:CAS RN-SMILES database/software?" (Jul 22, 7:49) References: <17F0D1642DC@msnet.mathstat.uoguelph.ca> Reply-To: Wolf-Dietrich.Ihlenfeldt@CCC.Chemie.Uni-Erlangen.DE X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: "Bill Kokiopoulos" Subject: Re: CCL:CAS RN-SMILES database/software? Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Jul 22, 7:49, Bill Kokiopoulos wrote: > Subject: CCL:CAS RN-SMILES database/software? > Hi my question are: > > > Is there any kind of database (ASCII file) or software > from which I can get SMILES representations of compounds > as an output by providing the corresponding CAS Registry > Numbers as an input? There are a number of online databases which support CAS number searching, but the only one which supports SMILES export (also for full hitlists as result of parallel multiple CASNO searches) seems to be the enhanced NCI database browser (http://www2.ccc.uni-erlangen.de/ncidb/ for Europe, http://cactvs.cit.nih.gov/ncidb/ for the US). Note that this database does not contain stereochemistry information. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From fgonzale@lauca.usach.cl Wed Jul 22 11:54:54 1998 Received: from ralun.usach.cl (ralun.usach.cl [158.170.64.21]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA15179 Wed, 22 Jul 1998 11:54:51 -0400 (EDT) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.8.5/8.8.8) with ESMTP id LAA03428 for ; Wed, 22 Jul 1998 11:54:35 -0400 (CST) Received: from lauca.usach.cl (kekule.usach.cl [158.170.16.6]) by lauca.usach.cl (8.6.12/8.6.12) with ESMTP id MAA28495 for ; Wed, 22 Jul 1998 12:04:21 -0400 Message-ID: <35B609AC.F5EF2EBC@lauca.usach.cl> Date: Wed, 22 Jul 1998 11:47:56 -0400 From: Danilo Gonzalez Organization: Universidad de Santiago de Chile X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: "chemistry@www.ccl.net" Subject: metallointercalators-complexes which bind to DNA Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi all! I'll give a lecture on "Charge Transfer through the DNA base stack". Does anybody know where to download 3D structures (PDB) of metallointercalators-complexes which bind to DNA by classical intercalation? Thanks a lot! Danilo/// -- Fernando Danilo González Nilo University of Santiago de Chile, Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago-CHILE Phone: (562) 681 2575-Anexo:799 ; Fax: (562) 681 2108 URL : http://quimbio.usach.cl/~danilo/ E-mail: fgonzale@lauca.usach.cl =================================================================== From xyn@ornl.gov Wed Jul 22 13:27:27 1998 Received: from aspen.lsd.ornl.gov (aspen.lsd.ornl.gov [134.167.140.14]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA22324 Wed, 22 Jul 1998 13:27:26 -0400 (EDT) From: xyn@ornl.gov Received: (qmail 12893 invoked by uid 29178); 22 Jul 1998 17:27:27 -0000 Date: 22 Jul 1998 17:27:26 -0000 Message-ID: <19980722172726.12892.qmail@aspen.lsd.ornl.gov> To: chemistry@www.ccl.net Subject: CFP: JCO Special Issue on Computational Biology THIRD CALL FOR PAPERS ====================== Journal of Combinatorial Optimization Special Issue on Computational Molecular Biology Guest Editors: Ying Xu, Satoru Miyano, Tom Head. Submission Deadline: August 15, 1998. The past ten years have witnessed the rapid development of a new discipline, computational molecular biology. Combinatorial optimization and algorithms have played a significant role in advancing this new discipline. The partnership between mathematics, in particular combinatorial optimization and algorithms, and molecular biology has greatly enriched both fields, leading to new ways of thinking and greater challenges to meet. The scope of this Special Issue includes all aspects of combinatorial optimization and algorithms in computational molecular biology. Original papers are solicited that describe research on combinatorial methods for problems arising from the following areas (nonexhaustive) of molecular biology: -- DNA sequencing -- DNA mapping -- recognition of genes and regulatory elements -- RNA/protein structure prediction -- molecular evolution -- combinatorial libraries and drug design -- bio-sequence analysis and comparison -- computing with biomolecules. Six hard copies of each submitted manuscript should be sent to one of the guest editors by August 15, 1998. Manuscripts must be prepared according to the normal submission requirements of the Journal of Combinatorial Optimization (see ). Each manuscript will be refereed by at least three anonymous reviewers. Notification of acceptance will be sent to the authors before November 30, 1998. The Special Issue is expected to be published by mid-1999. Addresses of the guest editors: Ying Xu Computational Biosciences Section Building 1060 COM Oak Ridge National Laboratory Oak Ridge, TN 37831-6480, USA Tel: 423-574-7263 Fax: 423-241-1965 Email: xyn@ornl.gov Web: Satoru Miyano Human Genome Center Institute of Medical Science University of Tokyo Shirokanedai 4-6-1, Minato-ku, Tokyo 108-8639, Japan. Tel.: +81-3-5449-5615 Fax: +81-3-5449-5442 Email: miyano@ims.u-tokyo.ac.jp Tom Head Department of Mathematics Binghamton University Binghamton, NY 13902-6000, USA Tel: 607-777-2278 Email: tom@math.binghamton.edu Web: From andrew@info.combichem.com Wed Jul 22 15:03:02 1998 Received: from hermes.combichem.com (hermes.combichem.com [207.158.48.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA01564 Wed, 22 Jul 1998 15:02:58 -0400 (EDT) Received: from info.combichem.com ([207.158.46.99]) by hermes.combichem.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-49457U200L100S0) with ESMTP id AAA383; Wed, 22 Jul 1998 11:58:32 -0700 Message-ID: <35B63603.A3E30CDB@info.combichem.com> Date: Wed, 22 Jul 1998 11:57:07 -0700 From: Andrew Smellie X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: amberLists , "APPLSPEC@uga.cc.uga.edu" , "CHEMCHAT@UAFSYSB.UARK.EDU" , "CHEMIG@LIST.NIH.GOV" , "CHEMISTRY@www.ccl.net" , "CHMINF-L@LISTSERV.INDIANA.EDU" , "ICS-L@UMDD.UMD.EDU" , "isisforum-l@mdli.com" , "listserver@ic.ac.uk" , "mailbase@mailbase.ac.uk" , "molecular-dynamics-news@mailbase.ac.uk" , "NATODATA@CC1.KULEUVEN.AC.BE" , "pdb-l@pdb.pdb.bnl.gov" Subject: Call for papers.... Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit SYMPOSIUM ANNOUNCEMENT AND SECOND CALL FOR PAPERS Conformational Analysis: Stepping up to the new challenges. to be held at the American Chemical Society Meeting in Anaheim, CA March 21-25, 1999 Sponsored by the Division of Computers in Chemistry The interest in processing millions of compounds from high-throughput screening and combinatorial or virtual libraries has placed new demands on the ability to conformationally analyze large numbers of molecules. Often the generation of good low-energy conformations for these large datasets is the major bottleneck in deducing 3D information from these molecules. This session focuses on models, tools and techniques for deriving 3D information from large numbers of molecules. The due date for 150 word abstracts is November 18, 1998. For planning purposes, however, please let me know if you plan to submit an abstract no later than August 15th, 1998. Dr. Andrew Smellie CombiChem Inc., 1804 Embarcadero Rd., Palo Alto, CA 94303 andrew@info.combichem.com (650)-842-0560 From topper@cooper.edu Wed Jul 22 17:12:14 1998 Received: from magnum.cooper.edu (magnum.cooper.edu [199.98.16.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA10764 Wed, 22 Jul 1998 17:12:08 -0400 (EDT) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA00220 (5.65c/IDA-1.4.4 for ); Wed, 22 Jul 1998 16:55:08 -0400 Received: by zeus.cooper.edu id AA22995 (5.67b/IDA-1.5 for chemistry@www.ccl.net); Wed, 22 Jul 1998 17:03:16 -0400 From: TOPPER ROBERT Message-Id: <199807222103.AA22995@zeus.cooper.edu> Subject: CCL:Summary:Followup Visualization To: chemistry@www.ccl.net Date: Wed, 22 Jul 1998 17:02:46 -0400 (EDT) Cc: topper@cooper.edu (TOPPER ROBERT) X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hello all, As promised, a summary. Thanks to those who replied! Robert ******************************************************************************** Robert Q. Topper Asst. Professor of Chemistry fax: (212) 353-4341 The Cooper Union phone: (212) 353-4378 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/ ******************************************************************************** The Cooper Union, established by Peter Cooper in 1859, is a private engineering/ architecture/art college where all students receive full scholarships. ******************************************************************************** ********************************************* The Original Question: ********************************************* Thanks to Jonathan for his summary. I am writing to seek clarification one one point. > 2. Import and display multiple small molecules in various styles (tube, > wireframe, etc.). I interpret this feature as the ability to display multiple molecules in various styles simultaneously. For example; a wireframe model of a protein surrounded by tube models of water molecules. What program(s) have this particular feature? This is a useful thing to be able to do, certainly. I will be glad to summarize for the list. ********************************************* RESPONSES: ********************************************* Sender: bruce@nmr.utmb.edu I'm pretty sure MOLMOL does this. Bruce Luxon =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Bruce A. Luxon, Ph.D Associate Professor Sealy Center for Structural Biology Dept. of Human Biological Chemistry & Genetics University of Texas Medical Branch Galveston, TX 77555-1157 (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ http://www.nmr.utmb.edu/ mailto:bruce@nmr.utmb.edu =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ********************************************* From: Sergei Izrailev Dear Dr. Topper: TOPPER ROBERT wrote: > I interpret this feature as the ability to display multiple molecules > in various styles simultaneously. For example; a wireframe model of > a protein surrounded by tube models of water molecules. > > What program(s) have this particular feature? This is a useful > thing to be able to do, certainly. > VMD can do it easily. See http://www.ks.uiuc.edu/Research/vmd/ Sincerely, Sergei Izrailev sergei@ks.uiuc.edu ********************************************* Sender: triche@cornell.edu Organization: Johnson Graduate School of Management To: TOPPER ROBERT Hey, a guy from Cooper Union! Pretty cool. I just found out about Cooper last night in the context of merit-based free education. I was happy to note that they have scientists and engineers as well as artists. Anyways, Data Explorer (with the Chemistry modules my old boss worked on, available from www.tc.cornell.edu/~richard via some link or other) can do this just fine. You make a pdb file of all the molec's you want and select the atoms for each style, shove them through the appropriate modules (surf, CPK, whatever), presto, all set. If you don't use something like DX this probably won't be real helpful. ********************************************* From mildred@houdini.tds-tds.com Wed Jul 22 17:17:53 1998 Received: from houdini.tds-tds.com ([207.99.16.200]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA10828 Wed, 22 Jul 1998 17:17:44 -0400 (EDT) Received: from houdini.tds-tds.com ([207.99.16.200]) by houdini.tds-tds.com (Netscape Mail Server v2.0) with SMTP id AAA6863; Wed, 22 Jul 1998 17:17:54 -0500 Date: Wed, 22 Jul 1998 17:17:53 -0400 (EDT) From: "Mildred R. Green PhD" To: Bill Kokiopoulos cc: chemistry@www.ccl.net Subject: Re: CCL:CAS RN-SMILES database/software? In-Reply-To: <17F0D1642DC@msnet.mathstat.uoguelph.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Mr Kokiopoulos: I can think of two such sources: For ASCII files there is the LOGKOW Database with over 19,000 CAS numbers and SMILES for over 19,000 chemicals. The alternative is an online service which TDS offers called QSAR which will output a CAS number and SMILES for about 23,000 chemicals. Please contact me if you need more information. Mildred Green ------------------------------------------------------------------------------ Technical Database Services, Inc (TDS) EMAIL: mrgreen@tds-tds.com Phone: 212 245 0044 FAX: 212 247 0587 WEBSITE: http://www.tds-tds.com ------------------------------------------------------------------------------ On Wed, 22 Jul 1998, Bill Kokiopoulos wrote: > Hi my question are: > > > Is there any kind of database (ASCII file) or software > from which I can get SMILES representations of compounds > as an output by providing the corresponding CAS Registry > Numbers as an input? > > If there exist such databases /software please let me > know which are they and how I can get them (maybe give > me a URL I can check out). > > Many Thanks > > Vassilios (Bill) Kokiopoulos > University of Guelph > > e-mail : bkokiopo@msnet.mathstat.uoguelph.ca > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: bkokiopo.MathStat.CPES.uoguelph@msnet.mathstat.uoguelph.ca > -- Original Sender From: Address: bkokiopo.MathStat.CPES.uoguelph@msnet.mathstat.uoguelph.ca > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From howardp@syrres.com Wed Jul 22 17:52:14 1998 Received: from apollo.syrres.com (apollo.syrres.com [204.168.121.242]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA11200 Wed, 22 Jul 1998 17:52:13 -0400 (EDT) Received: from pc-howardp.syrres.com ([204.168.121.208]) by apollo.syrres.com (Netscape Mail Server v2.0) with SMTP id AAA75; Wed, 22 Jul 1998 17:51:33 -0400 Message-Id: <3.0.32.19980722175617.00cb7be0@apollo.syrres.com> X-Sender: howardp@apollo.syrres.com X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 22 Jul 1998 17:56:17 -0400 To: "Bill Kokiopoulos" , chemistry@www.ccl.net From: howardp@syrres.com (Phil Howard) Subject: Re: CCL:CAS RN-SMILES database/software? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Bill, See http://esc.syrres.com/~esc1/smilecas.htm This has about 103,000 chemicals. Phil At 07:49 AM 7/22/98 -500, Bill Kokiopoulos wrote: >Hi my question are: > > > Is there any kind of database (ASCII file) or software > from which I can get SMILES representations of compounds > as an output by providing the corresponding CAS Registry > Numbers as an input? > > If there exist such databases /software please let me > know which are they and how I can get them (maybe give > me a URL I can check out). > > Many Thanks > > Vassilios (Bill) Kokiopoulos > University of Guelph > > e-mail : bkokiopo@msnet.mathstat.uoguelph.ca > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: bkokiopo.MathStat.CPES.uoguelph@msnet.mathstat.uoguelph.ca >-- Original Sender From: Address: bkokiopo.MathStat.CPES.uoguelph@msnet.mathstat.uoguelph.ca >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From gusev@javanet.com Wed Jul 22 21:31:25 1998 Received: from mail1.javanet.com (mail1.javanet.com [205.219.162.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA12598 Wed, 22 Jul 1998 21:31:24 -0400 (EDT) Received: from monaco (ct-hartford-us2233.javanet.com [209.150.36.96]) by mail1.javanet.com (8.8.8/8.7) with SMTP id VAA32198 for ; Wed, 22 Jul 1998 21:31:24 -0400 (EDT) Message-Id: <3.0.5.32.19980722213011.0090de10@mail.javanet.com> X-Sender: gusev@mail.javanet.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 22 Jul 1998 21:30:11 -0400 To: chemistry@www.ccl.net From: Vladimir Gusev Subject: Web examples of modeling lipid bilayers Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello CCL, I would appreciate any pointers to the modeling (MD or MC) of systems with lipid bilayers presented on the web. Thank you in advance. Vladimir