From chemistry-request@ccl.net Fri Oct 1 02:20:05 2004 Received: from mailfilter.diszk.unideb.hu ([193.6.138.70]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i917K485027598 for ; Fri, 1 Oct 2004 02:20:05 -0500 Received: from mailfilter.diszk.unideb.hu (localhost [127.0.0.1]) by mailfilter.diszk.unideb.hu (Postfix) with SMTP id 880879FEC4; Fri, 1 Oct 2004 09:31:04 +0200 (CEST) Received: from Cthulhu (anti309.chem.klte.hu [193.6.133.108]) by delfin.unideb.hu (Postfix) with SMTP id E12F3C802; Fri, 1 Oct 2004 09:30:59 +0200 (DFT) Message-ID: <004301c4a788$9aa0d940$6c8506c1@Cthulhu> From: "Tamas E. Gunda" To: , References: <1096462911.415ab23f28147_at_webmail.mta.ca> Subject: Re: CCL:advice requested regarding overlay software Date: Fri, 1 Oct 2004 09:31:02 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 You may try the fitting with Mol2Mol. It has options to include or not H atoms, to use different weight factors, to use a list of the atoms to be included in the fitting procedure (when the molecules are not identical). Batch calculations from multiple molecule files and output/conversion to a new file of the fitted, superimposed molecules are also possible. The rms deviations are also calculated. http://web.interware.hu/frenzy/mol2mol Hope this helps Dr. Tamas E. Gunda University of Debrecen Medical and Health Science Center Dept. of Pharmaceutical Chemistry Debrecen, Hungary e-mail: tgunda*AT*puma.unideb.hu ----- Original Message ----- From: To: Sent: Wednesday, September 29, 2004 3:01 PM Subject: CCL:advice requested regarding overlay software > Enzyme crystal structures lack hydrogens and usually contain inhibitors. Due > to the size of the crystal structures computing at a high level of theory with > different substrates is not feasible. It is our hope to be able to compute > fragments of the active site at high level of theory and combine them to a > realistic model. Is there a program which allows overlaying computed > geometries and experimental crystal structures using least squares fitting? > Any advice on how to compare computed with experimental to ensure maximum > overlap of the combined optimized fragments to the entire crystal. Is there a > way to ensure the orientation of the fragments as they would be in the crystal? > > Any advice would be greatly appreciated. > > Ken Hunter > Mount Allison University > > -= 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 Fri Oct 1 07:18:59 2004 Received: from mailfe01.swip.net (mailfe01.swip.net [212.247.154.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i91CIw90013354 for ; Fri, 1 Oct 2004 07:18:58 -0500 X-T2-Posting-ID: 442u/WtJiSHUAn31jJObTujyZw7dsLBiHq866AtC57s= Received: from [83.176.57.145] (HELO avdemo.tiscalinet.ch) by mailfe01.swip.net (CommuniGate Pro SMTP 4.2.3) with ESMTP id 173425683 for chemistry$at$ccl.net; Fri, 01 Oct 2004 14:29:53 +0200 Message-Id: <5.0.2.1.0.20041001142650.020eb920$at$mail.tiscalinet.ch> X-Sender: barry.hardy$at$mail.tiscalinet.ch (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Fri, 01 Oct 2004 14:27:42 +0200 To: chemistry$at$ccl.net From: Barry Hardy Subject: Poster submissions for Applications of Cheminformatics & Chemical Modelling to Drug Discovery Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=1.0 required=7.5 tests=MAILER_VERSION autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net The eCheminfo community conference "Applications of Cheminformatics & Chemical Modelling to Drug Discovery" takes place 8-19 November 2004. (See http://echeminfo.com/ for further information and to register.) We welcome Poster submissions in the following topic areas: Library Design, Virtual Screening, Docking, QSAR, Quality Control & Validation, Protein Modelling, Modelling of Membranes & Ion channels, QM/MM, Open Source, Grid Computing and Drug Design. All eCheminfo 2004 registrants and community members are eligible to submit a Conference Poster. Poster Abstracts (of ca. 300 words) with Title, Institution, Authors and Contact Information should be submitted to echeminfo$at$douglasconnect.com. Conference Posters can be presented as HTML, pdf, Powerpoint or Word documents. Posters must be submitted by 29th October. All accepted Posters will be eligible for the eCheminfo 2004 Best Poster Awards. Conference Brochure: http://conferences.metalayer.net/mch3/kBase/echeminfo/echem04programbrochure.pdf Conference Program (with abstracts & bios): http://conferences.metalayer.net/echeminfo/design/conference/html/speakerinfoechem.htm Community & Conference Blog (news & views): http://barryhardy.blogs.com/cheminfostream/ best regards Barry Hardy Barry Hardy, PhD Douglas Connect, Switzerland www.douglasconnect.com +41 61 851 0170 (office) Email: barry.hardy$at$tiscalinet.ch From chemistry-request@ccl.net Fri Oct 1 09:21:34 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 i91ELXlC020983; Fri, 1 Oct 2004 09:21:33 -0500 To: chemistry~at~ccl.net Cc: "Computational Chemistry List" Subject: Glasses for printed stereo imagaes MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy~at~givaudan.com Date: Fri, 1 Oct 2004 16:32:25 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 01/10/2004 16:32:34, Serialize complete at 01/10/2004 16:32:34 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 i91ELYlC020987 Dear Colleagues, Do you happen to know where one can buy special glasses for printed stereo images? Many thank, 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 Barry Hardy Sent by: "Computational Chemistry List" 01.10.2004 14:27 To: chemistry~at~ccl.net cc: Subject: CCL:Poster submissions for Applications of Cheminformatics & Chemical Modelling to Drug Discovery The eCheminfo community conference "Applications of Cheminformatics & Chemical Modelling to Drug Discovery" takes place 8-19 November 2004. (See http://echeminfo.com/ for further information and to register.) We welcome Poster submissions in the following topic areas: Library Design, Virtual Screening, Docking, QSAR, Quality Control & Validation, Protein Modelling, Modelling of Membranes & Ion channels, QM/MM, Open Source, Grid Computing and Drug Design. All eCheminfo 2004 registrants and community members are eligible to submit a Conference Poster. Poster Abstracts (of ca. 300 words) with Title, Institution, Authors and Contact Information should be submitted to echeminfo~at~douglasconnect.com. Conference Posters can be presented as HTML, pdf, Powerpoint or Word documents. Posters must be submitted by 29th October. All accepted Posters will be eligible for the eCheminfo 2004 Best Poster Awards. Conference Brochure: http://conferences.metalayer.net/mch3/kBase/echeminfo/echem04programbrochure.pdf Conference Program (with abstracts & bios): http://conferences.metalayer.net/echeminfo/design/conference/html/speakerinfoechem.htm Community & Conference Blog (news & views): http://barryhardy.blogs.com/cheminfostream/ best regards Barry Hardy Barry Hardy, PhD Douglas Connect, Switzerland www.douglasconnect.com +41 61 851 0170 (office) Email: barry.hardy~at~tiscalinet.ch -= 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 Fri Oct 1 17:52:06 2004 Received: from ms-smtp-01.nyroc.rr.com (ms-smtp-01.nyroc.rr.com [24.24.2.55]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i91Mq5IB027655 for ; Fri, 1 Oct 2004 17:52:05 -0500 Received: from rpi.edu (alb-24-195-20-186.nycap.rr.com [24.195.20.186]) by ms-smtp-01.nyroc.rr.com (8.12.10/8.12.10) with ESMTP id i91N2oZw002735; Fri, 1 Oct 2004 19:02:53 -0400 (EDT) Message-ID: <415DE219.EDA29EE5~at~rpi.edu> Date: Fri, 01 Oct 2004 19:02:50 -0400 From: "Curt M. Breneman" X-Mailer: Mozilla 4.8 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry~at~ccl.net, qsar_society~at~accelrys.com, chminf-l~at~listserv.indiana.edu Subject: Chemical Computing Group Excellence Awards - San Diego ACS Meeting Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: Symantec AntiVirus Scan Engine X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS 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 Computational Chemistry and Cheminfo folks, The ACS Division of Computers in Chemistry and the Chemical Computing Group (CCG) is pleased to invite applications for a new round of ten CCG Excellence Awards that provide travel funds and networking opportunities for graduate students presenting in a COMP (or COMP co-organized) symposium at the 229th National ACS Meeting in San Diego, California on March 13-17, 2005. In order to beconsidered for a CCG Excellence Award, you must send in the following items (electronic format is preferred) to me on or before Friday, October 23, 2004: 1) An extended (2-page) abstract of your oral or poster presentation. 2) A personal statement about your graduate and post-graduate career goals. 3) A letter of support from your dissertation advisor (this may be sent separately by the advisor). To qualify for an award, you must also submit your work to the ACS program prior to the COMP OASys abstract deadline of November 5, 2004. Winners will be announced after the OASys deadline date. See you in San Diego! Curt Breneman Professor of Chemistry and Chemical Biology RPI 110 8th St. Troy, NY 12180 brenec~at~rpi.edu From chemistry-request@ccl.net Fri Oct 1 12:23:52 2004 Received: from mhub-c2.tc.umn.edu (mhub-c2.tc.umn.edu [160.94.128.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i91HNpkl000863 for ; Fri, 1 Oct 2004 12:23:52 -0500 Received: from pobox.com (abacavir.pharmacy.umn.edu [160.94.172.208] (may be forged)) by mhub-c2.tc.umn.edu with ESMTP; Fri, 1 Oct 2004 12:34:48 -0500 (CDT) X-Umn-Remote-Mta: [N] abacavir.pharmacy.umn.edu [160.94.172.208] #+HF+LO+TS+AU Message-ID: <415D9621.9070007~at~pobox.com> Date: Fri, 01 Oct 2004 12:38:41 -0500 From: Eric Bennett User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP30; en-US; rv:1.4.1) Gecko/20040326 X-Accept-Language: en-us, en MIME-Version: 1.0 To: andras.borosy~at~givaudan.com, chemistry~at~ccl.net Subject: Re: CCL:Glasses for printed stereo imagaes 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=7.5 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 andras.borosy~at~givaudan.com wrote: >Dear Colleagues, > >Do you happen to know where one can buy special glasses for printed >stereo images? > >Many thank, > > Here is one source: http://www.hamptonresearch.com/hrproducts/4517.html -- Eric Bennett, Center for Drug Design, U of Minnesota From chemistry-request@ccl.net Fri Oct 1 16:31:47 2004 Received: from mail86-ash-R.bigfish.com (mail-ash.bigfish.com [206.16.192.253]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i91LVkkl019277 for ; Fri, 1 Oct 2004 16:31:46 -0500 Received: from mail86-ash.bigfish.com (localhost.localdomain [127.0.0.1]) by mail86-ash-R.bigfish.com (Postfix) with ESMTP id 64CD73606DE for ; Fri, 1 Oct 2004 21:42:53 +0000 (UCT) X-BigFish: VC Received: by mail86-ash (MessageSwitch) id 1096666973317007_4510; Fri, 1 Oct 2004 21:42:53 +0000 (UCT) Received: from mailrelay7.pfizer.com (ns11.pfizer.com [192.77.198.11]) by mail86-ash.bigfish.com (Postfix) with ESMTP id 394C33605DA for ; Fri, 1 Oct 2004 21:42:53 +0000 (UCT) Received: from groexms02.pfizer.com (localhost [127.0.0.1]) by mailrelay7.pfizer.com (Switch-3.0.5/Switch-3.0.0) with ESMTP id i91Lgl0o020942 for ; Fri, 1 Oct 2004 17:42:47 -0400 (EDT) Received: from groexcn04.pfizer.com (unverified) by groexms02.pfizer.com (Content Technologies SMTPRS 4.2.1) with ESMTP id for ; Fri, 1 Oct 2004 17:42:42 -0400 Received: by groexcn04.pfizer.com with Internet Mail Service (5.5.2654.89) id ; Fri, 1 Oct 2004 17:42:42 -0400 Message-ID: From: "Shanmugasundaram, Veerabahu" To: "'chemistry|at|ccl.net'" Subject: Call for papers - Applications of Information Theory in Chemistry . Date: Fri, 1 Oct 2004 17:42:35 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2654.89) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.5 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 229th National Spring ACS Meeting, San Diego, CA (March 13-17, 2005) Applications of Information Theory in Chemistry Co-sponsored by Chemical Information (CINF) & Computers in Chemistry (COMP) Divisions We invite you to submit an abstract for the symposium titled Applications of Information Theory in Chemistry at the upcoming Spring ACS National Meeting in San Diego. In 1948 Claude Shannon introduced a theory of communication, later known as the information theory, for measuring the transmission of information from a sender to a receiver across a noisy channel. This seminal work initially led to the development of an area of active research, primarily amongst mathematicians and engineers. However, more recently, a number of publications have appeared in the chemical and biological literature covering a wide range of applications, which include (but are not limited to) - 1. Origins of life and the evolution of biological information 2. Protein structure prediction and analysis of conformational ensembles of macromolecules 3. Discovery of DNA motifs, sequence analysis, target identification 4. Sensory coding neurons to understand their neurological functions 5. Analysis of descriptors, similarity and diversity of molecules and chemical libraries 6. Feature selection, QSAR and QSPR methods 7. Virtual screening applications and combinatorial library design 8. Analytical methods such as chromatography, proteomic gels 9. Experimental design and exploratory data analysis We plan to bring together a diverse group of researchers and scientists who have thought about and applied information theoretic principles to a variety of different chemical and biological problems. This will be an invited/contributed symposium. Please use the on-line abstract submission system (OASYS) for submitting your abstract () as per ACS guidelines. Submissions can be made through the CINF (for cheminformatic applications) or COMP (for computational chemistry applications) Divisions. The deadline for submitting abstracts for CINF is November 23, 2004 and for COMP is November 5, 2004. We also request that contributing authors (not invited authors) submit via email to us, an extended 1000-word abstract (in addition to the OASYS submission) with any references to their work, as the number of open positions are limited. Thank you, Veer & Gerry. Symposium co-chairs: Veerabahu Shanmugasundaram, Ph.D. Computer-Assisted Drug Discovery Pfizer Global Research & Development 2800 Plymouth Road Ann Arbor, MI 48105 Tel: (734) 622-7131 Fax : (734) 622-2782 Email: Veerabahu.Shanmugasundaram|at|pfizer.com Gerald M. Maggiora, Ph.D. Professor of Medicinal Chemistry Department of Pharmacology & Toxicology University of Arizona College of Pharmacy 1703 E. Mabel, P.O. Box 210207 Tucson AZ 85721-0207 USA (520) 626-5905 (Phone) maggiora|at|pharmacy.arizona.edu LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.