From chemistry-request@www.ccl.net Sat Oct 24 05:26:49 1998 Received: from prg.traveller.cz (prg.traveller.cz [193.85.2.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA18390 Sat, 24 Oct 1998 05:26:49 -0400 (EDT) Received: from winnt (prg71.login.cz [193.86.199.101]) by prg.traveller.cz (8.9.1.EUnet/8.9.ors) with SMTP id LAA07788 for ; Sat, 24 Oct 1998 11:26:48 +0200 (MET DST) Message-ID: <003801bdff31$dd6a3f10$65c756c1@winnt> Reply-To: "Jiri Krechl" From: "Jiri Krechl" To: Subject: Conversion 3D -> 2D Date: Sat, 24 Oct 1998 11:22:06 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Dear All, I am looking for a procedure that will be able to convert a set of Cartesian 3D coordinates into a collection of 2D pictures in some common format (SDfile, MOLfile, CamSoft.). Important condition is that the results should be "nice" in respect of regularity of cycles, obscuring of centers should be prevented etc. (option that is in most drawing packages satisfied by "clean" button) and most importantly, it would be able to handle batches, not just single 3D set. Any ideas and pointers please directly to jiri.krechl@spechem.cz Thanks Dr Jiri Krechl From chemistry-request@www.ccl.net Sat Oct 24 06:40:13 1998 Received: from uxmail.ust.hk (root@uxmail.ust.hk [143.89.14.30]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA18555 Sat, 24 Oct 1998 06:40:11 -0400 (EDT) Received: from chzm68.ust.hk ([143.89.55.138]:1449 "EHLO ust.hk" ident: "NO-IDENT-SERVICE") by uxmail.ust.hk with ESMTP id <627653-8406>; Sat, 24 Oct 1998 18:39:08 +0800 Message-ID: <36321F73.52BD4D8@ust.hk> Date: Sat, 24 Oct 1998 18:42:22 +0000 From: Zhenyang LIN Reply-To: chzlin@ust.hk Organization: Chemistry/HKUST X-Mailer: Mozilla 4.04 (Macintosh; I; 68K) MIME-Version: 1.0 To: "CHEMISTRY@www.ccl.net" Subject: Summary of Responses Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 8bit Dear CCLers, I am writing to thank those who have responded to my previous email in soliciting help to get some information on the successes of computational chemistry. The following are the responses I have got and I enclose them for your information. Sincerely yours, Zhenyang LIN/Chemistry/HKUST *************************************************************** 1. From: Juan Miguel Bocanegra Maybe a look at http://www.nobel.se/announcement-98/chemistry98.html and specially at the linked document http://www.nobel.se/announcement-98/chemback98.pdf can be a good starting point. I found this very interesting and suitable for non-theoretical chemists. -- 'Lord, let me tell you, let me tell you I really did the best I could.' --Plant/Page: Since I've been loving you Juan Miguel Bocanegra Moron (mailto:juanmi@blucher.qf.ub.es) Grup de Cinetica i Dinamica de Reaccions Elementals DEPARTAMENT DE QUIMICA FISICA-UNIVERSITAT DE BARCELONA Marti i Franques, 1 08023 Barcelona SPAIN tel: ++34 93 402-1224 http://www.qf.ub.es/area3/jbm.html 2. From: "JENSAB" If you hear about any succes stories within pharmaceutical research, please share them with us. I think the majority of pharmaceutical research is based on molecolar mechanics and not on quantum chemical calculations where the noble prize were given. In structural chemistry however look up our article in JACS: Unraveling the Electronic and Vibrational Contributions to Deuterium Isotope Effects on 13C Chemical Shifts by ab initio Model Calculations. Analysis of Isotope Effects on Sterically Perturbed Intramolecular Hydrogen Bonded o-Hydroxy Acyl Aromatics, Abildgaard, J.; Boldvig, S.; Hansen, P.E. J. Am. Chem. Soc. 1998, 120 (35), 9063. or in J. Phys. Chem: Molecular and Vibrational Structure of 1,6,6al4-Trithiapentalene. Infrared Linear Dichroism Spectroscopy and ab initio Normal Mode Analyses, Andersen, K. B.; Abildgaard, J.; Radziszewski, J. G.; Spanget-Larsen, J. J. Phys. Chem. Part A 1997, 101, 4475. Yours Sincerely Jens Abildgaard Department of Chemistry and the Life Sciences Roskilde University, Hus 18.2 Post Box 260, DK-4000 Roskilde, Denmark Telephone (+45) 46 74 29 52 Fax (+45) 46 74 30 11 3. From: "Dr. Klaus Stark" please have a look at http://www.msi.com/solutions/cases/appindex.html There you will find lots of computationsl chemistry application examples for materials and life science as well. Best regards Klaus Stark,PhD Application Scientist Molecular Simulations Inc. 230/250 The Quorum, Barnwell Road Cambridge CB5 8RE England E-Mail : kstark@msicam.co.uk Web Page : http://www.msi.com Catalysis Examples : http://www.msi.com/info/applications 4. From: Yun Tang Two years ago I wrote a review to the general public about the successful stories of computer-aided drug design in China, maybe it's helpful. Unfortunately it was written in Chinese. You can find it in your University Library. TANG Yun, JIANG Hua-Liang, CHEN Kai-Xian, JI Ru-Yun. Computer-aided drug design is trending towards success. ShengMin KeXue (Life Sci.) 1996; 8(4): 5-9. (in Chinese) Best regards, -- *********************************** Yun TANG, Ph.D. Center for Structural Biochemistry Department of Biosciences at Novum Karolinska Institute S-141 57 Huddinge Sweden *********************************** 5. From: "Preston J. MacDougall" In response to your request for some success stories, I know of a drug design company that does all their preliminary research on supercomputers, and they now have some drugs nearing FDA approval. They actually look at the Laplacian as part of their design strategy as well. There was a press release that has some information, at http://www.cybercasters.com/cwsa/Hausheer.html Good luck with your talk! Preston Preston J. MacDougall Assistant Professor Department of Chemistry, Box X101 Middle Tennessee State University Murfreesboro, TN 37132 6. From: Gregory Durst Don Boyd wrote a chapter in their book series of "Reviews in Computational Chemistry", on successes in computational chemistry in drug design that may interest you. The full reference is: "Reviews in Computational Chemistry", eds. K. Lipkowitz and D. Boyd, Wiley-VCH, NY, 1990, pp 355-371. regards, Greg Durst computational chemist Eli Lilly & Co. Indianapolis, IN USA 7. From: "Huff, Tom" Some of the information at these links might be useful to you. <> http://www.netsci.org/Science/Compchem/feature16.html <> http://www.msi.com/science/online/articles/catavis/CATAVIS.HTM <> http://www.msi.com/solutions/catalysis/index.html Tom Huff 8. From: "Boyd" You will find many examples of successful drug design in the following two references: Progress in Rational Design of Therapeutically Interesting Compounds. D. B. Boyd, in Rational Molecular Design in Drug Research, Proceedings of the Alfred Benzon Symposium No. 42, T. Liljefors, F. S. J¿rgensen, and P. Krogsgaard-Larsen, Eds., Munksgaard, Copenhagen, 1998, pp. 15-23. Innovation and the Rational Design of Drugs. D. B. Boyd, CHEMTECH, 28 (5), 19-23 (1998). Donald B. Boyd, Ph.D. Research Professor of Chemistry Editor, Reviews in Computational Chemistry Editor, Journal of Molecular Graphics and Modelling Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu Web http://chem.iupui.edu/rcc/rcc.html 9. From: jubert@nahuel.biol.unlp.edu.ar (Alicia Jubert) take a look at CHEMTECH, april 1998 page 18-22. You will see how AMOCO works. It's great!!! sincerely Alicia Jubert ******************************************************************** -- Zhenyang LIN Assistant Professor Chemistry Dept HKUST Fax no: (+852)23581594 email: chzlin@ust.hk http://home.ust.hk/~chzlin/