From chemistry-request@ccl.net Thu Nov 18 04:31:45 2004 Received: from web14102.mail.yahoo.com (web14102.mail.yahoo.com [216.136.172.132]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAI9ViMh012088 for ; Thu, 18 Nov 2004 04:31:44 -0500 Received: (qmail 21453 invoked by uid 60001); 18 Nov 2004 09:45:43 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=xjhImp5I3bmKq+MO3mpfRBMPGge4nwsN08qD0up2qXrlGy81dXxdfMZ8lhjcHvIIDCzk+SMLbUndgYD4m3stcK7u4+deYtS1lkRcSETZsarPX8A96v/2lg1FCgaYJCDvngILZYtpnlrNStn9i6/1V+La2JNVnFEiEfNlVpdX9yQ= ; Message-ID: <20041118094542.21451.qmail{at}web14102.mail.yahoo.com> Received: from [134.102.86.12] by web14102.mail.yahoo.com via HTTP; Thu, 18 Nov 2004 01:45:42 PST Date: Thu, 18 Nov 2004 01:45:42 -0800 (PST) From: raquel crespin Subject: About Thermochemistry data for aminoacids To: chemistry{at}ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS 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 members I am looking for a data of thermochemistry properties of aminoacids like formation, vaporization and solidification entalpies. Can you give some references? Thankful Rachel __________________________________ Do you Yahoo!? Meet the all-new My Yahoo! - Try it today! http://my.yahoo.com From chemistry-request@ccl.net Thu Nov 18 07:26:20 2004 Received: from cuces1.unisi.it (cuces1.unisi.it [193.205.4.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAICQIMh026425 for ; Thu, 18 Nov 2004 07:26:19 -0500 Received: from conversion_l.unisi.it by mailsrv.unisi.it (PMDF V6.2-X17 #30893) id <01LHDR5CV5I8942GME/at/mailsrv.unisi.it> for chemistry/at/ccl.net; Thu, 18 Nov 2004 13:40:40 +0200 (MET-DST) Received: from zoe.unisi.it (zoe.smin.unisi.it [172.16.54.58]) by mailsrv.unisi.it (PMDF V6.2-X17 #30967) with ESMTP id <01LHDR5CPAA492LB5Z/at/mailsrv.unisi.it> for chemistry/at/ccl.net; Thu, 18 Nov 2004 13:40:41 +0200 (MET-DST) Date: Thu, 18 Nov 2004 13:30:55 +0100 From: Andrea Tafi Subject: Fifth European Workshop in Drug Design X-Sender: tafi/at/mailsrv.unisi.it To: CCL Message-id: <5.2.0.9.0.20041118132940.0292f0a0/at/mailsrv.unisi.it> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Content-type: multipart/alternative; boundary="Boundary_(ID_Fz0njlJIj8fjmRPKpDjrqQ)" X-Spam-Status: No, hits=1.2 required=7.5 tests=HTML_20_30,HTML_FONTCOLOR_BLUE, HTML_FONT_BIG,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --Boundary_(ID_Fz0njlJIj8fjmRPKpDjrqQ) Content-type: text/plain; charset="iso-8859-1"; format=flowed Content-transfer-encoding: quoted-printable The University of Siena is pleased to announce the Fifth European Workshop in Drug Design to be held in Certosa di Pontignano (Siena), Italy, from May 27 - June 05, 2005. This workshop, which follows up the four very successful previous editions, held respectively in Cortona on May 1995, and in Siena on May 1998, June 2001 and May 2003, will feature about 20 well known researchers from the University and the Pharmaceutical Industry, including directors of research, working with a maximum number of 65 workshop participants. Participants will be divided into teams, each team led by a tutor, and will focus on solving concrete problems in drug design using high level hardware and software tools, including 20 workstations and a server contributed by SGI. Talks and case studies will be interdisciplinary, touching upon ligand/structure based drug design, in silico ADME, design and screening of virtual libraries, molecular modelling methodologies, cheminformatics/bioinformatics and synthetic feasibility, etc. Participation in the Fifth European Workshop in Drug Design is limited to 65 applicants, selected on the basis of individual experience. For more info see: www.unisi.it/EWDD On behalf of the Local Organizing Committee, Prof. Maurizio Botta Dipartimento Farmaco Chimico Tecnologico Universit=E0 degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234295 Fax: ++39 0577 234333 Email: direttore.dfct/at/unisi.it --Boundary_(ID_Fz0njlJIj8fjmRPKpDjrqQ) Content-type: text/html; charset="iso-8859-1" Content-transfer-encoding: quoted-printable
The University of Siena is pleased t= o announce the
Fifth European Workshop in Drug Design
to be held in Certosa di Pontignano (Siena), Italy, from
May 27 - June 05, 2005.
This workshop, which follows up the four very successful previous editions,
held respectively in Cortona on May 1995,
and in Siena on May 1998, June 2001 and May 2003,
will feature about 20 well known researchers from the University
and the Pharmaceutical Industry, including directors of research,
working with a maximum number of 65 workshop participants.
Participants will be divided into teams, each team led by a tutor,
and will focus on solving concrete problems in drug design
using high level hardware and software tools,
including 20 workstations and a server contributed by SGI.
Talks and case studies will be interdisciplinary, touching upon
ligand/structure based drug design,
in silico ADME,
design and screening of virtual libraries,
molecular modelling methodologies,
cheminformatics/bioinformatics and synthetic feasibility, etc.
 Participation in the Fifth European Workshop in Drug Design is limited to
 65 applicants, selected on the basis of individual experience.
For more info see: www.unisi.it/EWDD
On behalf of the Local Organizing Committee,
Prof. Maurizio Botta
Dipartimento Farmaco Chimico Tecnologico
Universit=E0 degli Studi di Siena
Via Aldo Moro
I-53100 Siena, Italy
Phone: ++39 0577 234295
Fax: ++39 0577 234333
Email: direttore.dfct/at/unisi.it
--Boundary_(ID_Fz0njlJIj8fjmRPKpDjrqQ)-- From chemistry-request@ccl.net Thu Nov 18 03:51:00 2004 Received: from nomina.net.lu.se (nomina.net.lu.se [130.235.132.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAI8owMh007392 for ; Thu, 18 Nov 2004 03:50:59 -0500 Received: from teokem.lu.se (atle.teokem.lu.se [130.235.1.29]) by nomina.net.lu.se (8.9.3/8.9.0) with ESMTP id KAA02627; Thu, 18 Nov 2004 10:06:54 +0100 (MET) Message-ID: <419C65B8.2040102$at$teokem.lu.se> Date: Thu, 18 Nov 2004 10:04:56 +0100 From: Patrik Rydberg User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.5) Gecko/20030925 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL CC: Jinsong Zhao Subject: Re: CCL:probe used in GRID References: <20041117193721.49864.qmail$at$web15401.mail.cnb.yahoo.com> In-Reply-To: <20041117193721.49864.qmail$at$web15401.mail.cnb.yahoo.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.9 required=7.5 tests=FCS_URI_NODOTS, FVGT_m_MULTI_ODD2,FVGT_m_MULTI_ODD3,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 Here's a list of all probes I know of and what they describe N3+ sp3 Amine NH3 cation N2+ sp3 Amine NH2 cation N2: sp3 NH2 with lone pair N2= sp2 Amine NH2 cation N2 Neutral flat NH2 eg amide N1+ sp3 Amine NH cation N1: sp3 NH with lone pair N1= sp2 Amine NH cation N1 Neutral flat NH eg amide NH= sp2 NH with lone pair N1# sp NH with one hydrogen N: sp3 N with lone pair N:= sp2 N with lone pair N:# sp N with lone pair N-: Anionic tetrazole N NM3 Trimethyl-ammonium cation O sp2 carbonyl oxygen O:: sp2 Carboxy oxygen atom O- sp2 phenolate oxygen O= O of SO4 or sulfonamide OH Phenol or carboxy OH O1 Alkyl hydroxy OH group OC2 Ether oxygen OES sp3 ester oxygen atom ON Oxygen of nitro group OS O of sulfone / sulfoxide OH2 Water OFU Furan oxygen atom C3 Methyl CH3 group C1= sp2 CH aromatic or vinyl PO4 PO4 phosphate dianion PO4H PO4H phosphate anion S1 Neutral SH group H Neutral hydrogen atom F Organic fluorine atom F- Fluoride anion CL Organic chlorine atom CL- Chlorine anion BR Organic bromine atom BR- Bromine anion I Organic iodine atom I- Iodine anion LI+ Lithium cation NA+ Sodium cation K+ Potassium cation RB+ Rubidium cation CS+ Caesium cation MG+2 Magnesium cation CA+2 Calcium cation xxxx Reserved for future use ZN+2 Zinc cation CU+2 Cupric copper cation FE+2 Ferrous iron cation FE+3 Ferric iron cation BOTH The amphipathic Probe DRY The hydrophobic Probe COO- Ionised alkyl carboxy group AR.COO- Ionised aryl carboxy group CONH2 Alkyl amide AR.CONH2 Aryl amide CONHR * Alkyl N-alkyl amide R.CONHR AR.CONHR * Aryl N-alkyl amide AR.CONHR AMIDINE Alkyl amidine R.C(NH2)2 AR.AMIDINE Aryl amidine AR.C(NH2)2 M-DIAMINE meta-diamino-benzene best regards Patrik Rydberg Jinsong Zhao wrote: > 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@M http://cn.rd.yahoo.com/mail_cn/tag/yisou/image/*http://image.yisou.com > 1G>MJG1000UW#,QE;"5gSJWTVz@)H]#! > http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/event/mail_1g/ > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -------------------------------------------------------------------- Patrik Rydberg Tel: +46-46-222 8236 Theoretical Chemistry Fax: +46-46-222 4543 Chemical Center, P.O.B 124 patrik.rydberg$at$teokem.lu.se S-221 00 Lund, Sweden http://www.teokem.lu.se/~patrik -------------------------------------------------------------------- From chemistry-request@ccl.net Thu Nov 18 02:03:44 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAI73fMh029956; Thu, 18 Nov 2004 02:03:41 -0500 To: Uwe Richter Cc: chemistry^at^ccl.net, "Computational Chemistry List" Subject: Re: CCL:Kekule structure asignment - again MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy^at^givaudan.com Date: Thu, 18 Nov 2004 08:12:45 +0100 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 18/11/2004 08:17:40, Serialize complete at 18/11/2004 08:17:40 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=2.0 required=7.5 tests=IMPRONONCABLE_1,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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iAI73iMh029970 Dear Mr. Richter For academic users MOLOC is free (www.moloc.ch). This is a molecular modeling package designed with emphasis on high interactivity and contains almost everything what is needed in computer-aided molecular design. Best regards, Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy^at^givaudan.com Uwe Richter Sent by: "Computational Chemistry List" 17.11.2004 17:45 To: chemistry^at^ccl.net cc: Subject: CCL:Kekule structure asignment - again 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.) -= 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) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Nov 18 11:29:08 2004 Received: from mail.ececs.uc.edu (mail.ececs.uc.edu [129.137.4.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAIGT7Mh014455 for ; Thu, 18 Nov 2004 11:29:07 -0500 Received: from localhost (localhost [127.0.0.1]) by mail.ececs.uc.edu (Postfix) with ESMTP id 7CA4FFF4 for ; Thu, 18 Nov 2004 11:43:08 -0500 (EST) Received: from mail.ececs.uc.edu ([127.0.0.1]) by localhost (mail.ececs.uc.edu [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 14029-01-15 for ; Thu, 18 Nov 2004 11:42:57 -0500 (EST) Received: from gatekeeper.ececs.uc.edu (gatekeeper.ececs.uc.edu [10.63.3.227]) by mail.ececs.uc.edu (Postfix) with ESMTP id C109BFEF for ; Thu, 18 Nov 2004 11:42:57 -0500 (EST) Received: from localhost (swamink@localhost) by gatekeeper.ececs.uc.edu (8.12.10+Sun/8.12.2/Submit) with ESMTP id iAIGgvAo027876 for ; Thu, 18 Nov 2004 11:42:57 -0500 (EST) X-Authentication-Warning: gatekeeper.ececs.uc.edu: swamink owned process doing -bs Date: Thu, 18 Nov 2004 11:42:56 -0500 (EST) From: Karthikeyan Swaminathan To: chemistry{at}ccl.net Subject: Linear Discriminant In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new at ececs.uc.edu X-Spam-Status: No, hits=3.0 required=7.5 tests=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 Hi, Can any of you point out some codes available free on the net for performing Linear Discriminant Classification of data. Other popular software packages are also welcome. Swaminathan, Karthikeyan Graduate Student, University of Cincinnati.