From chemistry-request@ccl.net Tue Nov 16 20:05:03 2004 Received: from mail.mdli.com (mail.mdli.com [208.200.221.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAH150gu001567 for ; Tue, 16 Nov 2004 20:05:00 -0500 Received: from exch-sl02.mdli.com (exch-sl02.mdli.com [172.16.3.10]) by mail.mdli.com (Postfix) with ESMTP id 4E27AB5EBB for ; Tue, 16 Nov 2004 17:18:54 -0800 (PST) Received: by exch-sl02.mdli.com with Internet Mail Service (5.5.2657.72) id ; Tue, 16 Nov 2004 17:18:54 -0800 Message-ID: From: Terry Wright To: CHEMISTRY_at_ccl.net Subject: 2nd Call for papers - ACS San Diego March 13-17, 2005 : Informa tics Challenges for Start-Up Companies Date: Tue, 16 Nov 2004 17:18:43 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4CC43.612987DC" X-Spam-Status: No, hits=2.9 required=7.5 tests=HTML_60_70, HTML_FONTCOLOR_UNKNOWN,HTML_FONT_BIG,HTML_MESSAGE,LINK_TO_NO_SCHEME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C4CC43.612987DC Content-Type: text/plain National ACS Meeting: San Diego March 13-17 2005 Informatics Challenges for Start-Up Companies Division of Chemical Information This symposium is intended for discussion of the unique informatics challenges facing start-up companies. Talks for this symposium may deal on any aspect of cheminformatics, bioinorganics, or management of other scientific information. This includes such topics as. 1) Managing information with limited resources (money and support staff) 2) Commercial versus customized information management systems for your workplace. 3) Making applications from different sources work together. 4) How to efficiently share information across different groups or departments 5) Integrating information with partners or other collaborators. 6) Standardizing hardware/software for increased efficiency. 7) Registration systems for internal databases Talks may focus on either solutions for these issues, or discussion of the problems that still confront organizations in informatics handling. Speakers are not limited to those working at start-ups. Anyone with knowledge in this area is welcome to submit an abstract. Until November 23, abstracts may be entered electronically, via the OASYS system on the ACS web site (www.oasys.acs.org), then select Division of Chemical Information (CINF). After that date or, if you have problems, please send abstracts directly to me (terryw_at_mdli.com). Thanks for your interest. Terry Terry Wright MDL Information Systems 14600 Catalina Street San Leandro, CA 94577 Phone: 510-357-2222 ext. 1392 Email: terryw_at_mdli.com ------_=_NextPart_001_01C4CC43.612987DC Content-Type: text/html

 

National ACS Meeting: San Diego   March 13-17 2005

 

Informatics Challenges for Start-Up Companies

Division of Chemical Information

 

This symposium is intended for discussion of the unique informatics challenges facing start-up companies. Talks for this symposium may deal on any aspect of cheminformatics, bioinorganics, or management of other scientific information. This includes such topics as.

 

1)   Managing information with limited resources (money and support staff)

2)   Commercial versus customized information management systems for your workplace.

3)   Making applications from different sources work together.

4)   How to efficiently share information across different groups or departments

5)   Integrating information with partners or other collaborators.

6)   Standardizing hardware/software for increased efficiency.

7)   Registration systems for internal databases

 

Talks may focus on either solutions for these issues, or discussion of the problems that still confront organizations in informatics handling. Speakers are not limited to those working at start-ups. Anyone with knowledge in this area is welcome to submit an abstract.

 

Until November 23, abstracts may be entered electronically, via the OASYS system on the ACS web site (www.oasys.acs.org), then select Division of Chemical Information (CINF). After that date or, if you have problems, please send abstracts directly to me (terryw_at_mdli.com).

 

Thanks for your interest.

 

Terry

 

 

Terry Wright

MDL Information Systems

14600 Catalina Street

San Leandro, CA 94577

 

Phone: 510-357-2222 ext. 1392

Email: terryw_at_mdli.com

 

------_=_NextPart_001_01C4CC43.612987DC-- From chemistry-request@ccl.net Wed Nov 17 09:26:14 2004 Received: from postag.jerini.de (defendo.jerini.com [62.206.112.102]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAHEQAOJ032483 for ; Wed, 17 Nov 2004 09:26:13 -0500 Received: from jerini.de ([192.168.0.161]) by postag.jerini.de (Lotus Domino Release 5.0.11) with ESMTP id 2004111715400700:55568 ; Wed, 17 Nov 2004 15:40:07 +0100 Message-ID: <419B627A.30303-.at.-jerini.de> Date: Wed, 17 Nov 2004 15:38:50 +0100 From: Uwe Richter User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry-.at.-ccl.net Subject: CCL: Kekule structure asignment X-MIMETrack: Itemize by SMTP Server on Server1Jerini/BioTools/DE(Release 5.0.11 |July 24, 2002) at 17.11.2004 15:40:07, Serialize by Router on Server1Jerini/BioTools/DE(Release 5.0.11 |July 24, 2002) at 17.11.2004 15:40:10, Serialize complete at 17.11.2004 15:40:10 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed X-Spam-Status: No, hits=3.9 required=7.5 tests=MY_BAD_DOT,NO_RDNS2 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 CCLers, does anybody know of a (preferably free) software which is able to assign correct Kekule structures to molecules just from the 3D coordinates (e.g. PDB file) and write this information into a something like a SD file? From the MM point of view this would mean assigning the correct atom type and protonation state from the interatomic distances and angles. Let's assume the structures in the PDB file are sufficiently accurate. Any help is greatly appreciated, Uwe From chemistry-request@ccl.net Wed Nov 17 09:37:46 2004 Received: from wrzx35.rz.uni-wuerzburg.de (wrzx35.rz.uni-wuerzburg.de [132.187.3.35]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAHEbiOJ001521 for ; Wed, 17 Nov 2004 09:37:45 -0500 Received: from wrzx34.rz.uni-wuerzburg.de (wrzx34.rz.uni-wuerzburg.de [132.187.3.34]) by wrzx35.rz.uni-wuerzburg.de (Postfix) with ESMTP id 4FA05DD1AA; Wed, 17 Nov 2004 15:51:41 +0100 (CET) Received: from virusscan (localhost [127.0.0.1]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id 2BA50AA40D; Wed, 17 Nov 2004 15:51:41 +0100 (CET) Received: from wrzx28.rz.uni-wuerzburg.de (wrzx28.rz.uni-wuerzburg.de [132.187.3.28]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id 0D4E0AA200; Wed, 17 Nov 2004 15:51:41 +0100 (CET) Received: from wac1006.chemie.uni-wuerzburg.de (wac1006.chemie.uni-wuerzburg.de [132.187.69.6]) by wrzx28.rz.uni-wuerzburg.de (Postfix) with ESMTP id A80D8D436B; Wed, 17 Nov 2004 15:51:40 +0100 (CET) Received: (from kaupp@localhost) by wac1006.chemie.uni-wuerzburg.de (8.11.2/8.11.2/SuSE Linux 8.11.1-0.5) id iAHEpe814230; Wed, 17 Nov 2004 15:51:40 +0100 From: Martin Kaupp Message-Id: <200411171451.iAHEpe814230^at^wac1006.chemie.uni-wuerzburg.de> Subject: CCL: Book on NMR/EPR parameter calculations To: chemistry^at^ccl.net Date: Wed, 17 Nov 2004 15:51:40 +0100 (CET) Cc: kaupp^at^mail.uni-wuerzburg.de, Vladimir Malkin , Michael Buehl X-Mailer: ELM [version 2.4ME+ PL60 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 X-Virus-Scanned: by amavisd-new (Rechenzentrum Universitaet Wuerzburg) X-Spam-Status: No, hits=1.9 required=7.5 tests=IMPRONONCABLE_2,MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iAHEbkOJ001528 ------------------------------------------------------------------ BOOK on quantum chemical calculations of NMR and EPR parameters: ------------------------------------------------------------------ Dear colleagues, For those of you interested in the rapidly growing field of computing magnetic resonance parameters by quantum chemical methods, we would like to point your attention to the following book, which has appeared this summer: "Calculation of NMR and EPR Parameters. Theory and Applications." (Eds. M. Kaupp, M. B|hl, V. G. Malkin), Wiley-VCH, 2004. (ISBN 3-527-30779-6) The book covers all essential aspects of the field in a concise manner, providing an overview and an entry into much of the literature in the field. For further information, please consult the publisher's web pages: http://www.wiley-vch.de/publish/dt/books/bySubjectCH00/ISBN3-527-30779-6/?sID=f0cc0b21d731b62110efe11e7f9ee8b7 or http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527307796.html or http://www.wiley.com/WileyCDA/WileyTitle/productCd-3527307796.html Sincerely, Martin Kaupp (W|rzburg, Germany), Michael B|hl (M|lheim, Germany), Vladimir G. Malkin (Bratislava, Slovakia) P.S.: For a few figures in the book that were printed in B&W, color versions may now be downloaded from: http://www.wiley-vch.de/templates/pdf/Kaupp_Farbabbildungen.pdf ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Prof. Dr. Martin Kaupp Institut f|r Anorganische Chemie Universitdt W|rzburg Am Hubland D-97074 W|rzburg Germany e-mail: kaupp^at^mail.uni-wuerzburg.de, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@ccl.net Wed Nov 17 07:24:31 2004 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAHCOUhs022810 for ; Wed, 17 Nov 2004 07:24:30 -0500 Received: by leitl.org (Postfix, from userid 500) id E43B83A84DB; Wed, 17 Nov 2004 13:38:25 +0100 (CET) Date: Wed, 17 Nov 2004 13:38:25 +0100 From: Eugen Leitl To: chemistry(at)ccl.net Subject: physorg: representation/simplification of many-electron calculations through two electrons Message-ID: <20041117123825.GK1457(at)leitl.org> Mime-Version: 1.0 http://www.physorg.com/news2000.html Breaking old barrier to better electron representation in molecular computations November 17, 2004 Results apply to fields ranging from medicine to superconductivity University of Chicago quantum chemist David Mazziotti has proposed a new research tool that could help scientists more rapidly solve problems in atmospheric chemistry, combustion, medicine and other areas of research where the behavior of electrons plays a key role. "We're in the pioneering stage so we're not going to go and treat all of these problems right away," said Mazziotti, an Assistant Professor in Chemistry. But with his new method, "we can do chemistry that cannot be done otherwise," he said. Mazziotti explains his method in the Nov. 19 issue of Physical Review Letters. Further details will follow in early December in the Journal of Chemical Physics. The key to understanding whether or not a particular chemical reaction will occur depends on a detailed statistical description of the electrons' positions in the molecules involved. Until now, scientists have found it necessary to attempt to represent the motion of all the electrons in the molecule of interest-a daunting task requiring vast quantities of computer power. "Just a single water molecule has 10 electrons," Mazziotti said. But in the 1950s, researchers theorized that it should be possible to accurately and more efficiently calculate the electronic properties of a molecule using only a pair of electrons representing many-even hundreds-of electrons in a molecular system. Mazziotti compares the feat to assembling a set of architectural blueprints, which represent in two dimensions a structure that can be built in three dimensions. An architect follows certain rules to ensure that a builder can translate a two-dimensional sketch into a three-dimensional structure. "In the same way atoms and molecules consist of many electrons, but there is a way to represent all of the electrons rigorously with only two electrons. Certain rules have to be followed to ensure the two-electron 'sketch' of the molecule accurately represents all the electrons in the atom or molecule," Mazziotti explained. Mazziotti's Physical Review Letters paper realizes a dream that scientists have pursued for 50 years by introducing a set of instructions for accurately and efficiently computing with a pair of electrons that represent the many electrons of the molecule. These instructions dramatically reduce the amount of computer time and memory required to compute the electronic properties of a molecule. Now Mazziotti can do some of the same calculations on his desktop computer that previously required Japan's Earth Simulator, the world's largest supercomputer. "David has really made a huge contribution in turning the dreams of 50 years ago into useful tools," said Bob Erdahl, a professor of mathematics at Queens University in Kingston, Ontario. Erdahl said Mazziotti's Physical Review Letters paper has applications to his own research in computing how behavior at the subatomic level brings about macroscopic changes in materials, such as the transition to the superconducting state. "I'm certainly going to look very closely and try to incorporate David's latest innovation into my work. I think we will very quickly be able to beat other approaches in this area of solids and compute things that were out of reach before," Erdahl said. Erdahl is especially interested in determining why superconductivity manifests itself only in two-dimensional layers rather than in three-dimensional solids. "The computations are of course very difficult to do. These methods that David is developing and that we're developing are very helpful in attacking that problem." While Erdahl works in mathematical physics, understanding the electronic energies that atoms and molecules possess also affects almost every area of chemistry. One such area, Mazziotti said, has broad applications includes the chemistry of free radicals-highly reactive unpaired electrons. In atmospheric chemistry, free radicals are instrumental in reactions leading to ozone depletion and the creation of greenhouse gases. Another area is the combustion of hydrocarbon fuels, which creates a variety of carbon-based radicals. "A lot of people want to know which radicals are present in a given combustion process and what reactions those were undergoing because that's going to affect fuel efficiency," Mazziotti said. A third area is medicine, because radical-type reactions are common in the human body. Mazziotti noted that hydroxy urea therapy combats sickle-cell anemia by forming a radical that triggers a cascade of additional reactions. "There is a 40 percent reduction in mortality for patients who receive hydroxy urea treatment for sickle cell," he said. Despite the advances that Mazziotti and others have contributed to the representation of electrons in atoms and molecules, further advances could be in the offing. He said the field is experiencing a new wave of research. "We're not done by any means." Source: University of Chicago -- Eugen* Leitl http://leitl.org ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net From chemistry-request@ccl.net Wed Nov 17 11:33:04 2004 Received: from postag.jerini.de (defendo.jerini.com [62.206.112.102]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAHGX4OJ012620 for ; Wed, 17 Nov 2004 11:33:04 -0500 Received: from jerini.de ([192.168.0.161]) by postag.jerini.de (Lotus Domino Release 5.0.11) with ESMTP id 2004111717470068:55841 ; Wed, 17 Nov 2004 17:47:00 +0100 Message-ID: <419B8038.3030600.-at-.jerini.de> Date: Wed, 17 Nov 2004 17:45:44 +0100 From: Uwe Richter User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry.-at-.ccl.net Subject: CCL: Kekule structure asignment - again X-MIMETrack: Itemize by SMTP Server on Server1Jerini/BioTools/DE(Release 5.0.11 |July 24, 2002) at 17.11.2004 17:47:00, Serialize by Router on Server1Jerini/BioTools/DE(Release 5.0.11 |July 24, 2002) at 17.11.2004 17:47:01, Serialize complete at 17.11.2004 17:47:01 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Dear colleagues, thanks for the responses so far. Apparently my question was not formulated clear enough. Having pdb files containing organic molecules but no connectivity records most programs (pymol,sybyl,cactus,babel,weblab viewer ...) are able to convert the structure to various formats. However, in most cases, multiple bonds, aromatic systems etc are not recognized (correctly) just > from the atomic coordinates. Thus a phenyl ring will turn up as cyclohexyl and so on. I am sure there is software around which can do this task properly. Thanks again, Uwe (I just tried MOE - no failures up to now, but this isn't exactly freeware.) From chemistry-request@ccl.net Wed Nov 17 14:23:34 2004 Received: from web15401.mail.cnb.yahoo.com (web15401.mail.cnb.yahoo.com [202.43.216.204]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAHJNSRE031567 for ; Wed, 17 Nov 2004 14:23:29 -0500 Message-ID: <20041117193721.49864.qmail..at..web15401.mail.cnb.yahoo.com> Received: from [219.144.206.196] by web15401.mail.cnb.yahoo.com via HTTP; Thu, 18 Nov 2004 03:37:21 CST Date: Thu, 18 Nov 2004 03:37:21 +0800 (CST) From: Jinsong Zhao Subject: CCL: probe used in GRID To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.5 required=7.5 tests=DATE_IN_PAST_12_24, MK_YAHOO_REDIR_01,WLS_URI_OPT_150 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 all, In GRID (ver 22, www.moldiscovery.com), I just kown the probe DRY is used to identify hydrophobic regions, and H or water probe, etc. However, I can not find the similar informaton for C3, C1= and many other probes. I mean the type of interaction between probe and ligand represented by the probe. Would you like to give me a brief description on this aspects or point me out where I can find those information. Additional question, where I can find the information about those probe, such as radius, charge and something else. Thank you very much for your consideration on this matter. Best wishes, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong..at..yahoo.com.cn _________________________________________________________ Do You Yahoo!? 150MrGzMP37h?qKQ#,4xDz43HkRt@V5nLC http://cn.rd.yahoo.com/mail_cn/tag/yisou/music/*http://music.yisou.com/ C..at..E.CwPGS&SP>!SP#,KQ1iC@MMJG1000UW#,QE;"5gSJWTVz@)H]#! http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/event/mail_1g/ From chemistry-request@ccl.net Wed Nov 17 14:09:49 2004 Received: from prg.traveller.cz (prg.traveller.cz [193.85.2.77]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAHJ9jRE030563 for ; Wed, 17 Nov 2004 14:09:46 -0500 Received: from Tata (pra-s29140.adsl.dial-up.cz [193.179.29.140]) by prg.traveller.cz (8.13.1/8.13.1/prg) with SMTP id iAHJNd08064811 for ; Wed, 17 Nov 2004 20:23:41 +0100 (CET) Message-ID: <003001c4ccda$f4575f00$6501a8c0@Tata> Reply-To: "Jiri Krechl" From: "Jiri Krechl" To: References: <20041117123825.GK1457..at..leitl.org> Subject: structures enumeration Date: Wed, 17 Nov 2004 20:20:57 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1250" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-Mimeole: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I am looking for a simple engine able to enumerate Markush structures, up to three substituents at once, with the following features: - output preferably SDFile - stand alone application reasonably priced (as it is required for one time / short time purpose) - able to run on PC under Windows Ability to handle substituents with two attachment points (variation of the cycles) will be highly appreciated. Guess it is not of general interest for the list subscribers, therefore kindly aim eventual responses directly to me. Many thanks Jiri --- Outgoing mail was checked virus free Zkontrolovano antivirov}m systimem AVG (http://www.grisoft.cz). Verze: 6.0.797 / Virova baze: 541 - datum vydanm: 15.11. 2004