From chemistry-request@server.ccl.net Thu Sep 30 15:51:11 1999 Received: from plains.NoDak.edu (root@plains.NoDak.edu [134.129.111.64]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA23142 for ; Thu, 30 Sep 1999 15:51:11 -0400 Received: from plains.nodak.edu (page.chem.ndsu.NoDak.edu [134.129.127.109]) by plains.NoDak.edu (8.9.3/8.9.3) with ESMTP id OAA30862 for ; Thu, 30 Sep 1999 14:44:14 -0500 (CDT) Message-ID: <37F3BD3D.7DB489BE@plains.nodak.edu> Date: Thu, 30 Sep 1999 14:42:56 -0500 From: michael page X-Mailer: Mozilla 4.51 (Macintosh; I; PPC) MIME-Version: 1.0 To: chemistry@ccl.net Subject: ACS Theory Subdiv./ Call for Apps Grad Student Comp. Awards Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit --Call for Applications IBM Graduate Student Awards in Computational Chemistry Below is an announcement for two Awards in Computational Chemistry that are open to current graduate students. We are grateful to IBM and the Minnesota Supercomputing Institute for their support of these awards. Let me urge you to encourage your graduate students to apply. The competition is open to any graduate student (regardless of citizenship) who began graduate study after August 1, 1996 and who is an ACS member (or whose advisor is an ACS member). These awards are designed to encourage graduate work in computational chemistry, to recognize research accomplishments, and to stimulate interest in the Subdivision of Theoretical Chemistry and the Physical Chemistry Division of the ACS. An Awards Committee will consider all the applicants. The awards applications should be sent to Ken Jordon at the University of Pittsburgh. Note that the deadline for applications is November 30. These two awards, supported by IBM, will provide one-time cash stipends of $2500 and $1000 as supplements to normal financial aid to doctoral candidates in the research-dissertation stage in the 1999-2000 academic year. The Minnesota Supercomputing Institute will provide each awardee up to 1000 node-hours on an IBM SP2 cluster for the awardees to actually carry out a portion of the awarded research. The awardees will have access to the consulting services of the Institute normally available to all users. Awardee selection will be made on a competitive basis. Applicants should be working on new and innovative computational chemistry methods or applications in theoretical chemistry. Applicants should prepare a written description of a computational chemistry research project that requires high performance computing, with an explanation of the scientific importance of the project. Proposals need to include an estimate of the computing resources required in SP2 cpu-hours. Applicants should explain how they plan to use the grant funds. Two letters of recommendation, including one from the student's advisor, along with a vita and transcript, are required. The proposal, including the vita, should not exceed five double-spaced pages. In addition, a faculty person (typically the applicant's research advisor) responsible for the applicant's use of the Minnesota Supercomputing Institute resources must be identified. Forward applications by November 30, 1999 to Prof. Ken Jordan Department of Chemistry University of Pittsburgh Parkman Ave. and University Drive Pittsburgh, PA 15260 JORDAN@a.psc.edu The awardees will be chosen in December. From chemistry-request@server.ccl.net Fri Oct 1 05:17:53 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA26630 for ; Fri, 1 Oct 1999 05:17:52 -0400 Received: from biochem.ucl.ac.uk (actually host bsmori1.biochem.ucl.ac.uk) by mail-b.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Fri, 1 Oct 1999 10:10:01 +0100 Received: from bsmir18.biochem.ucl.ac.uk (bsmir18 [128.40.46.21]) by biochem.ucl.ac.uk (8.9.2/8.9.1) with ESMTP id KAA13892 for ; Fri, 1 Oct 1999 10:10:07 +0100 (BST) Received: from localhost (nobeli@localhost) by bsmir18.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id KAA04965 for ; Fri, 1 Oct 1999 10:10:07 +0100 (BST) X-Authentication-Warning: bsmir18.biochem.ucl.ac.uk: nobeli owned process doing -bs Date: Fri, 1 Oct 1999 10:10:07 +0100 (BST) From: Irene Nobeli X-Sender: nobeli@bsmir18 Reply-To: Irene Nobeli To: Computational Chemistry List Subject: Re: molecular similation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all Some time ago I asked two questions. One was whether anyone knows of a database of all small molecules that can be found in cells, or the metabolome as I believe it is called. Unfortunately I received no answer to this question. My second question concerned software for determining molecular similarity (preferably available in the public domain). I am grateful to all the people who helped with their answers, which I copy below. Thank you all again, Irilenia >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From Christopher.Page@uv.es Mon Sep 13 16:37:01 1999 ...... Anyway, I have this program for doing similarity measurements/alignments, that was based on the original SEAL (Steric and Electrostatic ALignment) code of Kearsley and Smith. My program (called 'walrus') uses a much more sophisticated model for assessing the similarity, but this may be regarded as overkill for most cases (each calculation on a small molecule takes a few hours on an Octane; SEAL takes a few seconds) and is probably best restricted to calibration. It is also a pig to use. And it takes its input from Gaussian. But please let me know if you are interested. The SEAL code itself (fortran, but you need to make a couple of changes to get it to compile on an SGI) was supplied on a floppy disk with the original publication. I had all sorts of trouble getting this (floppy disks degrade quite quickly...), so, again, please let me know if you are interested. Good references to get you started are: @article{kears:seal, author = "S. K. Kearsley and G. M. Smith", title = "An alternative method for the alignment of molecular structures: maximising electrostatic and steric overlap", journal = "Tetrahedron Computer Methodology", volume = 3, pages = "615--633", year = 1990, note = "Includes original Fortran-77 source code for SEAL program."} @article{meyer:molecsim, author = "A. Y. Meyer and W. G. Richards", title = "Similarity of molecular shape", journal = "Journal of Computer-Aided Molecular Design", volume = 5, pages = "427--439", year = 1991} @article{richards:hrindex, author = "E. E. Hodgkin and W. G. Richards", title = "A semi-empirical method for calculating molecular similarity", journal = "Journal of the Chemical Society, Chemical Communications", pages = "1342--1344", year = 1986} @incollection{dean:drugs, author = "P. M. Dean", title = "Defining molecular similarity and complementarity for drug design", booktitle="Molecular Similarity in Drug Design", pages = "1--21", editor = "P. M. Dean", publisher="Chapman and Hall", address = "London", year = 1995} @incollection{good:drugs, author = "A. C. Good", title = "3D molecular similarity indices and their application in {QSAR} studies", booktitle="Molecular Similarity in Drug Design", pages = "1--21", editor = "P. M. Dean", publisher="Chapman and Hall", address = "London", year = 1995} Being nearby, you might also like to look in my thesis, which should be in the University of London library (C. S. Page, PhD, 1998). The final chapter ("Measuring Chirality") has a (fairly) comprehensive review. Hope this helps. best wishes, Chris Page Uni. Valencia >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From noronha@dedalus.lcc.ufmg.br Mon Sep 13 17:21:07 1999 ............... You could use the programs in New Arthur package, they are for clustering compounds using PCA, KNN and SIMCA methods, he is free. In order to calculate the phusico-chemical properties you could use WHIM 3D program he is also free and could be found in the inthernet to download, but has one problem, some parameters do'n't have physico-chemical significance, they are only mathematical. And you couldn't use them to derive QSAR models. You could also, finde COMFA for pc's free in the inthernet. I don't know any program that could calculate PLS and neural networks, two other clustering programs, inthe net for free, the are in TSAR package from Oxford Molecular. For generate equations, QSAR equations, I thing you could use the Bilin program, I think he is free too. I hope that could help you. If you're interested, my group here in Brazil has some good experience with clustering methods. If I could help more, let me know. Best Regards ___________________________________________________________________ | | |Antonio Luiz Oliveira de Noronha - noronha@dedalus.lcc.ufmg.br | |Medicinal Chemistry of Organotin Compounds | |NEQUIM - Medicinal Chemistry Group | |Chemistry Departament - DQ | |UFMG - Federal University of Minas Gerais - Brazil | |Av. Antonio Carlos, 6627 - Campus Pampulha | |CEP 31270-901 - Belo Horizonte - MG - Brazil | |VOICE +55 31 499 5765 - FAX +55 31 499 5700 | |___________________________________________________________________| >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From Yvonne.Martin@ln.ssw.abbott.com Mon Sep 13 22:09:16 1999 ............. You might want to look at two articles by Rob Brown and me: 1)Brown, R. D.; Martin, Y. C. Journal of Chemical Information and Compu= ter Sciences 1997, 37, 1-9. 2)Brown, R. D.; Martin, Y. C. Journal of Chemical Information and Compu= ter Sciences 1996, 36, 572-584. Also of course, there are many articles by Peter Willett on diversity. 1)Turner, D. B.; Tyrrell, S. M.; Willett, P. Journal Of Chemical Inform= ation And Computer Sciences 1997, 37, 18-22. and a whole issue of PD3 devoted to the topic. Attached are a couple of my articles. 1)Martin, Y. C. Perspectives in Drug Discovery and Design 1997, 7/8, 15= 9-172. 2)Martin, Y. C.; Brown, R. D.; Bures, M. G. "Quantifying Diversity"; Ke= rwin, J. F. and Gordon, E. M., Ed.; Wiley: New York, 1998, pp 369-385. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From noronha@dedalus.lcc.ufmg.br Tue Sep 14 12:43:03 1999 ................. I was wondering, there is another kind of physico-chemical parameters that you could use in QSAR. They are called quantum descriptors, and you could use GAMESS, that are free ab initio program to calculate them Best Regards >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From Dave.Winkler@molsci.csiro.au Thu Sep 30 01:50:06 1999 .............. >From what I heard at an AAPS meeting in Washington recently, the BCUT molecular diversity measures are good at clustering molecules with similar targets. These derive from some work on molecular eigenvalue indices first published by Frank Burden in J. Chem. Inf. Comput. Sci. in the late 80s aand turned into the Diverse Solutions software by Bob Pearlman at Uni Texas. I believe Tripos Associates (http://www.tripos.com) sell the software or Pearlman may release it to academic researchers. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From noronha@dedalus.lcc.ufmg.br Thu Sep 30 20:51:36 1999 ............ Dra. Irene Nobeli The WHIM 3D program you could dounload at this site: www.disat.unimi.it/chm The New Arthur package is a package for clustering analysis emploing SIMCA analysis, KNN and PCA, this cluster programs are all included. Do you have some experience with this kind of cluster algoritm? You could contact Dr. Bruns at this mail : bruns@iqm.unicamp.br Bilin is a program to perform bilinear analysis, correlating your biological activity with the phisico-chemical parameters. CoMFA - SoMFA you should search in the ccl homepage. There you will find where you could get this program. He perform a comparative field analysis QSAR 3D with your data and the biological activity. I hope this could help. Please fell free to ask questions that you have! Best Regards ___________________________________________________________________ | | |Antonio Luiz Oliveira de Noronha - noronha@dedalus.lcc.ufmg.br | |Medicinal Chemistry of Organotin Compounds | |NEQUIM - Medicinal Chemistry Group | |Chemistry Departament - DQ | |UFMG - Federal University of Minas Gerais - Brazil | |Av. Antonio Carlos, 6627 - Campus Pampulha | |CEP 31270-901 - Belo Horizonte - MG - Brazil | |VOICE +55 31 499 5765 - FAX +55 31 499 5700 | |___________________________________________________________________| ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Darwin Building Gower Street London WC1E 6BT nobeli@biochem.ucl.ac.uk 0171-419 3890 0171 504 2171 >>> The gene pool could use a little chlorine. <<< From chemistry-request@server.ccl.net Fri Oct 1 07:28:17 1999 Received: from mailimailo.univ-rennes1.fr (mailimailo.univ-rennes1.fr [129.20.131.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA27923 for ; Fri, 1 Oct 1999 07:28:15 -0400 Received: from ensc-rennes.fr (balaban.rech.ensc-rennes.fr [129.20.16.67]) by mailimailo.univ-rennes1.fr (8.9.3/jtpda-5.3.1) with ESMTP id NAA15361 for ; Fri, 1 Oct 1999 13:20:57 +0200 (MET DST) Sender: david@univ-rennes1.fr Message-ID: <37F498B6.E586D3C7@ensc-rennes.fr> Date: Fri, 01 Oct 1999 13:19:18 +0200 From: David Enot X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: chemistry@ccl.net Subject: (no subject) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am interested in finding out what academic research groups are involved in developing and using neural networks algorithms for QSPRfor molecular modeling and property prediction of lipids or any amphiphiles aggregation. Thanks you From chemistry-request@server.ccl.net Fri Oct 1 08:36:47 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA28231 for ; Fri, 1 Oct 1999 08:36:47 -0400 Received: from sctmg02.sct.ucarb.com ([140.170.101.20] (may be forged)) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id IAA01861 for ; Fri, 1 Oct 1999 08:29:36 -0400 (EDT) Received: by sctmg02.sct.ucarb.com with Internet Mail Service (5.5.2448.0) id ; Fri, 1 Oct 1999 08:31:41 -0400 Message-ID: <47F7EAA0389AD011840500805FEAB9C60376E31A@sctms01.sct.ucarb.com> From: "Fulton CR (Charles)" To: "'CCL'" Subject: Summary: Chemistry on Linux Date: Fri, 1 Oct 1999 08:31:34 -0400 Hello, On 9/15/99 I posted this question to the CCL: >Anyone know of any sites listing all open source comp. chemistry related >programs and code that runs on linux? I'm trying to compile a list. Here is a summary (well a list of lists really) that I have put together. thanks, -Charlie. SAL-Scientific Applications on Linux http://sal.kachinatech.com/sal1.shtml (us-mirror) (category list link) http://sal.kachinatech.com/Z/2/index.shtml (us-mirror) (Chemistry, Biology, & Related) Best starting point probably. Might be the only one you need to use. sort of like the "freshmeat.net" for scientific applications. one of the most recommended in the reply's. Linux and Chemistry 197 entries as of 30 Sep 1999, 19:54 http://chpc06.ch.unito.it/chem_linux.html Another excellent site. Exactly what I was looking for. Very nice site, good searching, easy navigation - broken up into nice categories Shows license (free, gpl, commercial, or shareware). This was also highly recommended in the reply's. Network Science Corporation: http://www.netsci.org/ Computational Chemistry articles : http://www.netsci.org/Science/Compchem/top.html "NetSci's Lists of Computational Chemistry Software" : http://www.netsci.org/Resources/Software/top.html I found some pretty nice articles here. They also have a software list broken down into categories. Opensource site: http://www.openscience.com/ most notably for the Jmol & JChemPaint projects. Molecular Biology related programs for Linux: http://evolution.bmc.uu.se/~thomas/mol_linux/index.html others: http://nmr400a.mols.susx.ac.uk/~steven/linux.html http://www.linuxlinks.com/Software/Scientific/ General Linux Application Resources: Linuxberg: http://irnet.Linuxberg.com/ Freshmeat: http://www.freshmeat.net/ General: http://www.linuxapps.com/ ---------------------------- Charles Fulton Catalyst Skill Center Adv. Information Technician Union Carbide Corporation S. Charleston, WV p:(304-747-3175) From chemistry-request@server.ccl.net Fri Oct 1 10:19:34 1999 Received: from gerwazy.chem.uni.wroc.pl (gerwazy.chem.uni.wroc.pl [156.17.103.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA28740 for ; Fri, 1 Oct 1999 10:19:25 -0400 Received: from wchuwr.chem.uni.wroc.pl ([156.17.103.1]) by gerwazy.chem.uni.wroc.pl (8.8.8+Sun/8.8.8) with ESMTP id QAA25587 for ; Fri, 1 Oct 1999 16:03:09 +0200 (MET DST) Received: from WCHUWR/SpoolDir by wchuwr.chem.uni.wroc.pl (Mercury 1.43); 1 Oct 99 15:57:09 MET Received: from SpoolDir by WCHUWR (Mercury 1.43); 1 Oct 99 15:54:38 MET From: "Andrzej Szymoszek" Organization: University of Wroclaw (Chemistry) To: chemistry@ccl.net, ASZYM@WCHUWR.CHEM.UNI.WROC.PL Date: Fri, 1 Oct 1999 15:54:35 MET Subject: CCL:anisole derivatives ab initio Priority: normal X-mailer: Pegasus Mail v3.40 Message-ID: Ladies and Gentlemen: I am looking for published ab initio results for anisole itself and para-substituted molecules H3C-O-C6H4X (X=H, Cl, F, NO2, NH2, OH or even second methoxy group). Sincerely, Andrzej Szymoszek aszym@wchuwr.chem.uni.wroc.pl Chemistry Department University of Wroclaw, Poland From chemistry-request@server.ccl.net Fri Oct 1 11:27:31 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA29051 for ; Fri, 1 Oct 1999 11:27:31 -0400 Received: from hugh.chem.uic.edu (HUGH.CHEM.UIC.EDU [131.193.195.93]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id LAA09340 for ; Fri, 1 Oct 1999 11:20:19 -0400 (EDT) Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id LAA06203; Fri, 1 Oct 1999 11:21:10 -0500 Date: Fri, 1 Oct 1999 11:21:03 +36000 From: Richard Wood cc: "'CCL'" Subject: Re: CCL:Summary: Chemistry on Linux In-Reply-To: <47F7EAA0389AD011840500805FEAB9C60376E31A@sctms01.sct.ucarb.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Well, with the "new millenium" (not really) about to start, I guess that now is the time for lists? Who are the 100 best CCL'ers of the century? R. From chemistry-request@server.ccl.net Fri Oct 1 12:31:17 1999 Received: from elsnycs18518.elsevier.com (elsnycs18518.elsevier.com [206.137.72.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA29344 for ; Fri, 1 Oct 1999 12:31:14 -0400 Received: from elsnycs18517.elsevier.com (elsnycs18517.elsevier.com [206.137.75.37]) by elsnycs18518.elsevier.com (2.6 Build 1 (Berkeley 8.8.6)/8.8.4) with ESMTP id MAA29644; Fri, 01 Oct 1999 12:22:29 +0100 Received: from elsnycs18678.elsevier.com (exch.elsevier.com [206.137.75.31]) by elsnycs18517.elsevier.com (2.6 Build 1 (Berkeley 8.8.6)/8.8.4) with ESMTP id MAA00104; Fri, 01 Oct 1999 12:23:00 +0100 Received: by exchange.elsevier.com with Internet Mail Service (5.5.2448.0) id ; Fri, 1 Oct 1999 12:22:21 -0400 Message-ID: <7B2BD12DCFD0D211A3B70008C707D73B160C1F@elsnycs18680.elsevier.com> From: "Glover, Jonathan (ELS)" To: "'chemistry@ccl.net'" Subject: Drug Design Conference Date: Fri, 1 Oct 1999 12:22:23 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" re previous posting 'Drug Design Conference' Regarding yesterday's announcement of Innovative Computational Applications: The Interface of Library Design, Bioinformatics, Structure Based Drug Design, and Virtual Screening, conference to be held October 25-27, 1999, The Sir Francis Drake Hotel, San Francisco, California, we ask that registrants please state the PRIORITY CODE when registering : P0459EM. Visit meeting website at OR, call or email Ellen Lubman, Director for this meeting at (212)661-3500 ext 3153 or elubman@iirny.com. This is a must-attend session for individuals seeking to develop programs and protocols within their companies which integrate bioinformatics and chemoinformatics. Top computational scientists present and explore pragmatic solutions instrumental to integrating biological and chemical data. Featured Keynote Address: * DOCKING & SCORING Irwin "Tack" Kuntz, Ph.D. Director, Molecular Design Institute UNIVERSITY OF CALIFORNIA- SAN FRANCISCO