From chemistry-request@ccl.net Fri Jan 23 09:05:33 2004 Received: from fikus.jh-inst.cas.cz (fikus.jh-inst.cas.cz [147.231.28.135]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0NE5Ujs028114 for ; Fri, 23 Jan 2004 09:05:31 -0500 Received: from fikus.jh-inst.cas.cz (root@localhost) by fikus.jh-inst.cas.cz (8.9.3/8.9.3/Debian/GNU) with local id PAA12821 for chemistry)at(ccl.net; Fri, 23 Jan 2004 15:07:01 +0100 Received: from tracy.jh-inst.cas.cz (tracy.jh-inst.cas.cz [147.231.28.129]) by fikus.jh-inst.cas.cz (8.9.3/8.9.3/Debian/GNU) with ESMTP id PAA12769 for ; Fri, 23 Jan 2004 15:06:56 +0100 Received: from TRACY/SpoolDir by tracy.jh-inst.cas.cz (Mercury 1.48); 23 Jan 04 15:07:02 +0200 Received: from SpoolDir by TRACY (Mercury 1.48); 23 Jan 04 15:06:53 +0200 Received: from uochb.cas.cz (147.231.29.220) by tracy.jh-inst.cas.cz (Mercury 1.48) with ESMTP; 23 Jan 04 15:06:44 +0200 Message-ID: <40112A6E.3070002)at(uochb.cas.cz> Date: Fri, 23 Jan 2004 15:06:38 +0100 From: "Mgr. Lubos Vrbka" Reply-To: lubos.vrbka)at(uochb.cas.cz Organization: IOCB User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20030916 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry)at(ccl.net Subject: water diffusion constants Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Masca-Timestamp: Fri, 23 Jan 2004 15:07:01 +0100 [fikus.jh-inst.cas.cz] X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL'ers, I'm looking for papers showing theoretically calculated water diffusion constants for low temperatures (up to ~270K) - I'm particularly interested in values for SPC/E water model but also in experimental data and data for other theoretical water models. I've seen the papers of Watanabe et al. (Chem. Phys. 131, 157, 1989) and Berendsen et al. (J. Phys. Chem. 91, 6269, 1987) but they do not contain much of the information I need... Mahoney et al. (J. Chem. Phys. 114, 363, 2001) is good hit, but is concerned mainly in TIP4P waters. Any help is greatly appreciated. Kind regards, Lubos -- ..................................................... Mgr. Lubos Vrbka Center for Complex Molecular Systems and Biomolecules Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic ..................................................... From chemistry-request@ccl.net Fri Jan 23 11:32:35 2004 Received: from vreme.yubc.net (vreme.yubc.net [212.124.160.13]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0NGWXjs005786 for ; Fri, 23 Jan 2004 11:32:34 -0500 Received: (from root@localhost) by vreme.yubc.net (8.11.6/8.11.6) id i0NGY5u00857 for CHEMISTRY..at..ccl.net; Fri, 23 Jan 2004 17:34:05 +0100 Date: Fri, 23 Jan 2004 17:34:05 +0100 From: workshop..at..vreme.yubc.net Message-Id: <200401231634.i0NGY5u00857..at..vreme.yubc.net> Subject: Invitiation to Madrid Workshop on Advanced Web Engineering for E-Business To: CHEMISTRY..at..ccl.net X-Spam-Status: No, hits=0.3 required=7.0 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear VIP of the Science: I am happy to invite you to be a speaker at the industrial workshop organized by IPSI BgD (Internet, Processing, Systems, and Interdisciplinaries), to be held in Madrid, Spain on March 21, 2004. Details on the web http://www.internetconferences.net A strong and innovative reviewing process providing a high quality feedback is a major asset of this workshop. See the web for details. This workshop takes place in one of the most exclusive hotels of the region, and is aimed at bringing together the most successful scientists of the field. Workshop covers applicative research of interest for industry, but participants are invited both from industry and academia. Please submit your title/abstract (which means that you have committed to participate if your paper is accepted), as soon as convenient for you, because we will be accepting papers only until the limit is reached. Only 20 presentations will be accepted, and only the first 60 submitted papers will be taken into consideration. The major goal of this forum is to establish a podium for a fruitful exchange of the newest scientific ideas, and that is why your participation is extremely important to all of us. As already indicated, only elite researchers and professionals are invited. If you like to accept this invitation, please send email (with title, abstract, and affiliation) to the email address workshop..at..vreme.yubc.net Conditions of this invitation are as follows: 1. Duration of your slot is 20 minutes (15 minutes for your talk, and the rest for discussion). 2. You are financially responsible: (a) for the air ticket to arrive (b) for the hotel/breakfast cost (you can stay in any hotel that you select) (c) for the workshop fee (e200) (d) all other expenses that you may have during the trip. 3. The workshop fee is e200. It covers a professional reviewing process, the workshop program, a book of abstracts, a CD with full papers, coffee/tea in the morning, a small working lunch in the early afternoon, and nothing else. 4. For the paper layout format, you are free to select any format that meets your needs and esthetical criteria. Your paper will be reviewed, with the major intention to provide you with a feedback that can help improve the quality. 5. Full papers are limited to maximum 1MBytes and minimum 4 pages. 6. The scope of the workshops is relatively wide, with Advanced Web Engineering as the common denominator. The stress is on interaction of participants who address the issue > from different angles, so all the following aspects are welcome: Informatics, Internet, Computer Science and Engineering, Interdisciplinary Research, MBA, Internet aspects of Medicine, Education, Management, Law, etc. Of course, traditional Electrical and Computer Engineering, and Engineering Physics, or BioEngineering and Environment Protection, too. Topic of special interest: Environment protection! Please note that our workshop AWEEB-2004 is the first one in the series of important meetings to take place during the same time period in Spain/Portugal: IADIS Applied Computing in Lisbon, Portugal, March 23-26, 2004. http://www.iadis.org/WBC2004/ ETAPS 2004 - The European Joint Conferences on Theory and Practice of Software, March 27 - April 2, 2004. http://www.lsi.upc.es/etaps04/ By attending AWEEB-2004 Madrid, you can also take adventage of the Saturday Rule (cheap air tickets); For the night before and the night after, Hotel Ritz charges only one half of the regular price (privilege of attendees of AWEEB-2004 Madrid). * * * * * Deadlines: Abstract (100 words) = January 31, 2004 Full Papers = February 15, 2004 Paper Acceptance Notification = February 20, 2004 Payment (fee and hotel) = February 25, 2004 Sincerely yours, Prof. Dr. Veljko Milutinovic, Chairman PS: If you like that we inform you about our other conferences (6 emails per year, for 12 conferences), please let us know. We will be informing you ONLY if you explicitely tell us that you like that to happen. Please, reply to workshop..at..vreme.yubc.net if you have questions or to confirm your desire to be a member of our VIP CLUB! From chemistry-request@ccl.net Fri Jan 23 11:39:48 2004 Received: from ccl.net (email.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0NGdljs005981 for ; Fri, 23 Jan 2004 11:39:47 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id i0NGfKXu004812; Fri, 23 Jan 2004 11:41:20 -0500 Date: Fri, 23 Jan 2004 11:41:24 -0500 (EST) From: Jan Labanowski To: chemistry..at..ccl.net, Andras.Borosy..at..givaudan.com Subject: QSAR - electron density based superposition Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ---------- Forwarded message ---------- From: Andras.Borosy..at..givaudan.com To: Computational Chemistry List NB: Unless you reset the To: line, your reply goes to the entire list --- Dear Colleagues, Does a (validated) computer application exist which can align molecules based on their electron density? Many thank, Andras Borosy PhD Computational Chemist Givaudan Schweiz AG Fragrance Research Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy..at..givaudan.com _______________________________________________ qsar_society mailing list qsar_society..at..accelrys.com http://ftp2.accelrys.com/mailman/listinfo/qsar_society From chemistry-request@ccl.net Fri Jan 23 12:20:24 2004 Received: from mxout6.cac.washington.edu (mxout6.cac.washington.edu [140.142.33.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0NHKKjs008295 for ; Fri, 23 Jan 2004 12:20:21 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout6.cac.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id i0NHLvMO007182; Fri, 23 Jan 2004 09:21:57 -0800 Received: from u.washington.edu ([128.95.128.116]) (authenticated bits=0) by smtp.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id i0NHLuS5003896 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Fri, 23 Jan 2004 09:21:57 -0800 Message-ID: <401157D2.6090308!at!u.washington.edu> Date: Fri, 23 Jan 2004 18:20:18 +0100 From: Carsten Detering User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031114 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Renxiao Wang CC: chemistry!at!ccl.net Subject: Re: CCL:Marketed drugs by structure-based design? References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Renxiao, One review I can think of the top of my head is Donald B. Boyd, Successes of Computer-Assisted Molecular Design, pp. 355-371., 1990 It is a little outdated, but nevertheless mentions four drugs that made it to the market. Hope this helps, Carsten Renxiao Wang wrote: > Hi, all! > > Would anybody please provide some references for marketed drugs whose > development were largely aided by structure-based design methods? Some > review papers/books must have mentioned this, but I cannot recall any at > this moment. > > Any clue is appreicated. I will put back the summary. Thanks in > advance! > > Regards, > > > > -------------------------------------------------------------------------------------------------- > Renxiao Wang, Ph.D. > Research Investigator > Department of Internal Medicine, Hematology/Oncology Division > University of Michigan Medical School > Ann Arbor, MI 48109, U.S.A. > Tel: (734) 764-2449; Fax: (734) 764-2532 > E-mail: renxiao!at!med.umich.edu > Web: http://sw8.im.med.umich.edu/~arthur/ > -------------------------------------------------------------------------------------------------- > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY!at!ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST!at!ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow!at!nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- Carsten Detering, Ph.D. University of Washington Department of Chemistry Box 351700 Seattle, WA 98195-1700 Fon 206.543.5081 Fax 206.685.8665 From chemistry-request@ccl.net Fri Jan 23 16:43:04 2004 Received: from marcy.nas.nasa.gov (marcy.nas.nasa.gov [129.99.113.17]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0NLh3js020976 for ; Fri, 23 Jan 2004 16:43:03 -0500 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.7p1+Sun/8.11.7/NAS-6n) with ESMTP id i0NLiXQ18020 for ; Fri, 23 Jan 2004 13:44:41 -0800 (PST) Date: Fri, 23 Jan 2004 13:44:33 -0800 (PST) From: Ioana Cozmuta To: Computational Chemistry List Subject: oxygen positions around a DNA Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi ccl users, Could anyone point me to some references that discuss what are the optimal position of oxygen molecules around a DNA strand? Thank you, Ioana From chemistry-request@ccl.net Fri Jan 23 12:53:52 2004 Received: from electra.cc.umanitoba.ca (electra.cc.umanitoba.ca [130.179.16.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0NHrpjs010546 for ; Fri, 23 Jan 2004 12:53:51 -0500 Received: from capella.cc.umanitoba.ca (server_at_capella.cc.umanitoba.ca [130.179.16.13]) by electra.cc.umanitoba.ca (8.12.10/8.12.10) with ESMTP id i0NHtNF9013760; Fri, 23 Jan 2004 11:55:25 -0600 (CST) Received: (from server@localhost) by capella.cc.umanitoba.ca (8.12.10+Sun/8.12.2) id i0NHtNl8014238; Fri, 23 Jan 2004 11:55:23 -0600 (CST) Received: from net118.chem.umanitoba.ca ( [net118.chem.umanitoba.ca]) as user schrecke@localhost by webware.cc.umanitoba.ca with HTTP; Fri, 23 Jan 2004 11:55:23 -0600 Message-ID: <1074880523.4011600b9caf6_at_webware.cc.umanitoba.ca> Date: Fri, 23 Jan 2004 11:55:23 -0600 From: "H. Georg Schreckenbach" To: chemistry_at_ccl.net Cc: schrecke_at_cc.UManitoba.CA Subject: summary: "easy" literature on modelling of bio-molecules? MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.1 X-Originating-IP: 130.179.49.38 X-Spam-Status: No, hits=1.1 required=7.0 tests=MAILTO_TO_SPAM_ADDR autolearn=no version=2.61 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Here is, as promised, my summary. Many thanx to all who replied! Best regards, Georg From: Alan Grossfield One good possibility would be "Molecular modellling: principles and applications", by Andrew Leach. The second edition came out in 2001, and it covers most areas of molecular modelling, including ab initio calculations, molecular mechanics, molecular dynamics and monte carlo, a smattering of advanced techniques, and some informatics type stuff. ---- This book was also recommended by a number of other people. I don't copy all of these replies here. GS. ---- From: Kenny Lipkowitz A book series I co-edit has a lot of tutorials and reviews on various aspects of computational chemistry beyond what one might find in traditional books onmolecular modeling. The series is called Reviews in Computational Chemistry, published by Wiley and has about 20 volumes now. From: Wayne Steinmetz I developed a large library in preparation for a course in molecular modeling. Here are two texts: a) A. R. Leach, Molecular Modelling, 2nd. ed. ,Prentice-Hall,2001, ISBN 0-582-38210-6. This was the text for the course. It provides the best overall coverage of the field. b) T. Schlick, Molecular Modeling and Simulation, Springer, 2000. ISBN 0-387-95404-X. Schlick takes an unusual multidisciplinary approach and combines insights from molecular biology, biophysics, and mathematics. From: Aldo Jongejan Just some books I thought of: Allen & Tildesley - Computer Silmulation of Liquids (Fortran code) Oxford University Press (Clarendon Press) ISBN 0-19-855375-7 ISBN 0-19-855645-4 (pbk) D. Rappaport - The Art of Molecular Dynamics (C code) Daan Frenkel & Berend Smit - Understanding Molecular Simulation ISBN: 0122673514 Andrew Leach - Molecular Modelling, Principles and Appications (no programming, but general introduction to modelling) From: "Michael A. Wilson" I think what he is trying to do is a monumentally difficult task, if only becuase there are so many different aspects to consider. One question, of course, is what does he hope to accomplish? Does he think that no CS types have thought about and contributed to the development of existing modeling codes? Or that computational chemistry, physics and biology are not informed by recent advances in computer science? Having said that, I guess some of the standard texts on modeling, such as "Allen and Tildesley" or "Hockney and Eastwood" would be a good place to start. -- Dr. H. Georg Schreckenbach Department of Chemistry, University of Manitoba Winnipeg, MB, R3T 2N2, Canada phone: (+204) 474-6261 FAX: (+204) 474-7608 http://home.cc.umanitoba.ca/~schrecke/ ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/