From chemistry-request@server.ccl.net Thu Apr 6 18:43:27 2000 Received: from mcdc-us-smtp3.cdc.gov (mcdc-us-smtp3.cdc.gov [198.246.96.74]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA09464 for ; Thu, 6 Apr 2000 18:43:26 -0400 Received: from mcdc-us-ims.cdc.gov (mcdc-us-imsgate.cdc.gov [198.246.96.17]) by mcdc-us-smtp3.cdc.gov with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.10) id 2MQHXPTJ; Thu, 6 Apr 2000 18:41:21 -0400 Received: by mcdc-us-imsgate.cdc.gov with Internet Mail Service (5.5.2448.0) id <2L3J52AF>; Thu, 6 Apr 2000 18:41:23 -0400 Message-ID: From: "Poda, Gennady" To: "'chemistry@ccl.net'" Subject: CCL: QSAR Software Summary Date: Thu, 6 Apr 2000 18:41:13 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id SAA09465 Hi, some time ago I posted a question about possible alternatives to the traditional Tripos and Oxford Molecular QSAR software suites. Here it is the answers. You migh wish to take a look at the following: http://www.models.kvl.dk/source/ http://www.eslc.vabiotech.com/ http://www.cris.com/~Hyposoft/ http://www.lnh.unil.ch/ http://www.scivision.com/sciQSAR.html http://www.pharma.ethz.ch/qsar/ Thanks a lot for your contribution. Happy QSARing! Gennady Poda 1--------------------------------------------------------------------------- From: bill email [hayden@chemcomp.com] Sent: Wednesday, March 22, 2000 11:10 AM To: Poda, Gennady; chemistry@ccl.net Subject: CCL:QSAR software Hi. Try Chemical Computing Group at; http://www.chemcomp.com Thanks, Bill Hayden 2------------------------------------------------------------------------- From: Jordi Villà [jorgevil@usc.edu] Sent: Tuesday, March 21, 2000 4:05 PM To: Poda, Gennady Subject: Re: CCL:QSAR software take a look at MIPSIM (http://www1.imim.es/mipsim). It generates molecular fields based on quantum mechanical calculations or on the GRID program, in order to be used along with GOLPE, for example. 3------------------------------------------------------------------------- From: Doug Henry [Dough@mdli.com] Sent: Tuesday, March 21, 2000 12:59 PM To: 'Poda, Gennady' Cc: Doug Henry Subject: RE: QSAR software Here's a few: Jay Ponder group home page: http://dasher.wustl.edu/ Alex Tropsha's web server: http://mmlin1.pha.unc.edu/~jin/QSAR/ Statlib archive: http://lib.stat.cmu.edu/ Recursive partitioning page: http://www.Recursive-Partitioning.com/ PLS toolbox code: http://www.models.kvl.dk/source/ WEKA datamining system: http://www.cs.waikato.ac.nz/ml/weka/ RSC Molecular modeling group: http://www.rsc.org/lap/rsccom/dab/software.htm CCC Erlangen website: http://www2.ccc.uni-erlangen.de/research/drugdesign/ Bayesian modeling: http://www.cs.berkeley.edu/~murphyk/Bayes/bnsoft.html http://www.cs.toronto.edu/~radford/fbm.software.html http://www.cs.cmu.edu/~javabayes/Home/index.html Autoclass-c: http://ic-www.arc.nasa.gov/ic/projects/bayes-group/autoclass/autoclass-c-pro gram.html The R package (like S): http://www.fas.umontreal.ca/BIOL/Casgrain/en/labo/R/index.html and of course, the QSAR and Modeling home page. Doug Henry MDL Information Systems Dough@mdli.com 4----------------------------------------------------------------------- From: Suleyman Bahceci [sbahceci@hotmail.com] Sent: Wednesday, March 22, 2000 2:52 PM To: gep4@cdc.gov Subject: Re: CCL:QSAR software Dear Dr. Poda, I would like call your attention to our methods which is not yet commercialized but published in the following publications: Bersuker, I. B.; Bahceci, S.; Boggs, J. E. The Electron-Conformational Method of Identification of Pharmacophore and Anti-Pharmacophore Shielding. In Pharmacophore Perception, Development, and Use in Drug Design, Guner, O. F. Ed.; International University Line, 2000; La Jolla, pp. 457-474. Bersuker, I. B.; Bahceci, S.; Boggs, J. E.; Pearlman, R. S. An Electron-Conformational Method of Identification of Pharmacophore and Anti-Pharmacophore Shielding. Application to Rice Blast Activity, J. Comput.-Aided Mol. Des., 1999, 13, 419-434. Bersuker, I. B.; Bahceci, S.; Boggs, J. E.; Pearlman, R. S. A Novel Electron-Conformational Approach to Molecular Modeling for QSAR by Identification of the Pharmacophore and Anti-Pharmacophore Screening, SAR and QSAR in Environmental Research, 1999, 10, 157-173. Best regards, Suleyman Bahceci, Ph.D. Department of Chememistry and Biochemistry The University of Texas at Austin 5---------------------------------------------------------------------- From: John S Tokarski [john.tokarski@bms.com] Sent: Tuesday, March 21, 2000 12:28 PM To: Poda Gennady Subject: Re: CCL:QSAR software Gennady, The software 4D-QSAR. ref: Hopfinger, A.J. et. al. "Construction of 3D-QSAR Models Using the 4D-QSAR Analysis Formalism", JACS, 1997, Vol. 119, 43, 10509-10524 contact Tony Hopfinger at hopfingr@uic.edu Regards, John "Poda, Gennady" wrote: > Dear CCLers, > > I am trying to collect information about QSAR software alternative to > well-known suites of Tripos and Oxford Molecular (mainly chemometrics, > freeware or for a reasonable price). > > So I would appreciate if you could site any competitive program (web site?) > which can do good QSAR work (NNs, GAs, PLS, GOLPE, etc.) with a good > descriptor set, variable selection/pruning/data preprocessing and model > validation (LOO, cross-validation, etc.). Any hints will be highly > appreciated. > > I will post a summary. > > Thanks a lot for your participation. > > Gennady Poda > > NIOSH/CDC > E-mail: gep4@cdc.gov > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- John S. Tokarski, Ph.D Research Investigator II Computer-Assisted Drug Design Department of Structural Biology and Modeling Bristol-Myers Squibb Pharmaceutical Research Institute MS H2307, P.O. Box 4000, Princeton, NJ 08543-4000 PH: (609)252-6154 FAX: (609)252-6030 EMAIL: john.tokarski@bms.com For UPS or FedEx: Rt. 206 and Provinceline Road, Lawrenceville, NJ 08648 From chemistry-request@server.ccl.net Fri Apr 7 00:58:42 2000 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA10639 for ; Fri, 7 Apr 2000 00:58:37 -0400 From: quanta@chem.unipune.ernet.in Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id KAA29697 for ; Fri, 7 Apr 2000 10:18:54 +0530 Received: (from quanta@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) id KAA08762 for CHEMISTRY@www.ccl.net; Fri, 7 Apr 2000 10:51:32 +0530 Date: Fri, 7 Apr 2000 10:51:32 +0530 Message-Id: <200004070521.KAA08762@chem.unipune.ernet.in> To: CHEMISTRY@server.ccl.net Subject: HYDROPHOBIC HYDRATION April 06, 2000 Can anyone please tell me the fundamental and other related references dealing with HYDROPHOBIC HYDRATION . Thanks in advance ANANT From chemistry-request@server.ccl.net Fri Apr 7 04:28:59 2000 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA11686 for ; Fri, 7 Apr 2000 04:28:58 -0400 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id KAA76993 for ; Fri, 7 Apr 2000 10:49:56 +0200 (CEST) Date: Fri, 7 Apr 2000 10:49:56 +0200 From: Christian Pilger To: chemistry@ccl.net Subject: AutoDock parameters for Br, Cl, F In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CClers, I'm going to dock several inhibitors which are comprised of C, N, H, O, S, but also of Br, Cl, F. When I started to modify the gpf- and dpf-Files to introduce the latter elements I noticed that there are differences in the parameters between those published on the AutoDock- webpage (which were used with AutoDock 2.4) and the parameters employed by the scripts mkgpf3 and mkdpf3 for all elements. Example: parameters for carbon carbon parameters used in mkgpf3 parameters used with AutoDock 2.4 map 1b41_07.C.map C.map nbp_r_eps 4.00 0.0222750 12 6 #C-C lj nbp_r_eps 4.00 0.1500 12 6 #C-C equilibrium separation and well-depth nbp_r_eps 3.75 0.0230026 12 6 #C-N lj nbp_r_eps 3.75 0.1549 12 6 #C-N equilibrium separation and well-depth nbp_r_eps 3.60 0.0257202 12 6 #C-O lj nbp_r_eps 3.60 0.1732 12 6 #C-O equilibrium separation and well-depth nbp_r_eps 4.00 0.0257202 12 6 #C-S lj nbp_r_eps 4.00 0.1732 12 6 #C-S equilibrium separation and well-depth nbp_r_eps 3.00 0.0081378 12 6 #C-H lj nbp_r_eps 3.00 0.0548 12 6 #C-H equilibrium separation and well-depth There is a constant factor 6.734 between the well-depths (3rd cols)of the new parameters compared to the old parameters (12-6-potential). I was unable to find an eplanation for this. Can anybody help me ? Cheers, Christian ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Apr 7 09:28:29 2000 Received: from morse.cancres.nottingham.ac.uk (morse.cancres.nottingham.ac.uk [128.243.118.199]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA13738 for ; Fri, 7 Apr 2000 09:28:27 -0400 Received: from morse.cancres.nottingham.ac.uk (localhost [127.0.0.1]) by morse.cancres.nottingham.ac.uk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA11932 for ; Fri, 7 Apr 2000 14:28:14 +0100 Sender: charlie@nottingham.ac.uk Message-ID: <38EDE26D.794B@nottingham.ac.uk> Date: Fri, 07 Apr 2000 14:28:13 +0100 From: Charlie Laughton Organization: University of Nottingham X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Comp Chem Lab Design Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, I have the opportunity to design from scratch a new comp. chem. facility of about 50 sq. m. Our current layout is very basic - just desking against the walls. It would be nice to have something that created a more inspiring environment. I would be interested to hear from other members of the list who have experience of successful (and unsuccessful!) designs as to what sort of layouts can work well. Regards, Charlie -- --------------------------------------------------------------------------- Dr Charlie Laughton | Lecturer in Drug Design and Discovery | Phone: (+44) 115 951 3405 School of Pharmaceutical Sciences | Fax: (+44) 115 951 3412 University of Nottingham | Email: Nottingham NG7 2RD | charles.laughton@nottingham.ac.uk UK | --------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Apr 7 11:08:34 2000 Received: from ibsprive.ibs.fr (pseudo7253.ibs.fr [192.134.37.253]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA14263 for ; Fri, 7 Apr 2000 11:08:14 -0400 Received: from ibs.fr (mjfield@lmspc4.ibs.fr [192.134.37.223]) by ibsprive.ibs.fr (8.8.8/8.8.8) with ESMTP id RAA29392 for ; Fri, 7 Apr 2000 17:08:41 +0200 (MET DST) Sender: mjfield@ibs.fr Message-ID: <38EDFA5B.C36ECF50@ibs.fr> Date: Fri, 07 Apr 2000 17:10:19 +0200 From: "Martin J. Field" X-Mailer: Mozilla 4.08 [en] (X11; I; Linux 2.0.35 i686) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: Dynamo Simulation Library Version 2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, We would like to announce the release of version 2 of the Dynamo simulation library. The library is free and may be downloaded from: http://www.ibs.fr/ext/labos/LDM/projet6/welcome_fr.htm Full details of the capabilities of the library and documentation are to be found on the web page. On behalf of the authors: Martin Field. --------------------------------------------------- Martin J. Field Laboratoire de Dynamique Moleculaire Institut de Biologie Structurale - Jean-Pierre Ebel 41, rue Jules Horowitz 38027 Grenoble Cedex 1 FRANCE Tel: (33)-4-76-88-95-94 Fax: (33)-4-76-88-54-94 Email: mjfield@ibs.fr --------------------------------------------------- From chemistry-request@server.ccl.net Fri Apr 7 11:43:44 2000 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA14481 for ; Fri, 7 Apr 2000 11:43:43 -0400 Received: from sally.schrodinger.com (shenkin@sally.schrodinger.com [166.84.149.25]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id IAA03814 for ; Fri, 7 Apr 2000 08:43:30 -0700 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.8/8.8.5) with ESMTP id LAA19676 for ; Fri, 7 Apr 2000 11:43:29 -0400 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Fri, 7 Apr 2000 11:43:28 -0400 (EDT) From: Peter Shenkin To: chemistry@ccl.net Subject: Re: CCL:Comp Chem Lab Design In-Reply-To: <38EDE26D.794B@nottingham.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Dear All, > > I have the opportunity to design from scratch a new comp. chem. facility > of about 50 sq. m. Our current layout is very basic - just desking > against the walls. It would be nice to have something that created a > more inspiring environment. Hi, How about hanging some test-tubes and beakers from the ceiling to remind us of our ancient roots in physical reality? :-), -P. On Fri, 7 Apr 2000, Charlie Laughton wrote: -- ** Whether the playing field is level depends on the coordinate system. *** ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@server.ccl.net Fri Apr 7 12:05:22 2000 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA14674 for ; Fri, 7 Apr 2000 12:05:08 -0400 Received: from cts.iitkgp.ernet.in (cts.iitkgp.ernet.in [144.16.192.220]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id VAA29694 for ; Fri, 7 Apr 2000 21:35:26 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id VAA09379 for ; Fri, 7 Apr 2000 21:24:51 +0530 Date: Fri, 7 Apr 2000 21:24:51 +0530 (IST) From: Rajarshi Guha To: CompuChem List Subject: Re: CCL:Comp Chem Lab Design Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 7 Apr 2000, Charlie Laughton wrote: > Dear All, > > I have the opportunity to design from scratch a new comp. chem. facility > of about 50 sq. m. Our current layout is very basic - just desking > against the walls. It would be nice to have something that created a > more inspiring environment. > Does'nt a comp chem lab just need computers? =============================================================== Rajarshi Guha | ...but there was no one Dept. of Chemistry | in it........ IIT Kharagpur. | | RG. email: rajarshi@presidency.com | rajarshi@cts.iitkgp.ernet.in | web : www.psynet.net/jijog | =============================================================== From chemistry-request@server.ccl.net Fri Apr 7 16:25:22 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA16665 for ; Fri, 7 Apr 2000 16:25:21 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id NAA02578 for ; Fri, 7 Apr 2000 13:23:31 -0700 (PDT) Received: from jnauss-pc.msi.com(146.202.26.50) by mailhost via smap (V2.0) id xmaa02572; Fri, 7 Apr 00 13:23:16 -0700 Message-Id: <4.3.0.20000407130347.00b082d0@146.202.6.217> X-Sender: jnauss@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Version 4.3 Date: Fri, 07 Apr 2000 13:05:32 -0400 To: chemistry@ccl.net From: Jeff Nauss Subject: MSI Workshops on NMR Techniques in May Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Molecular Simulations Inc. will be holding a pair of workshops focusing on NMR techniques at Rutgers University, New Brunswick, NJ. These workshops are currently the only NMR workshops scheduled in the US for 2000. Space is limited. On May 16-17, the "Biomolecular NMR: Processing and Analysis Workshop" will be held. This is an introductory course that addresses aspects of NMR data processing, display, and analysis of NMR culminating in the generation of specific NMR-based restraints using FELIX. On May 18-19, the "Biomolecular NMR: Structure Determination Workshop" will be given. This course addresses the generation, refinement, and evaluation of structures based upon NMR data using NMR X-PLOR and other modules. Different methods of structure generation using NMR restraints are discussed, as well as methods for evaluating the quality of structures. CNX will also be introduced. Knowledge of routine NMR data collection and analysis techniques is expected. Attendees should have either taken the "Introduction to Life Science Modeling with Insight II Workshop" or have experience with the Insight II interface. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for both courses and receive a 25% discount for the second workshop. Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's website (http://www.msi.com/about/events/training). Please do not hesitate to contact me should you have any questions. Thank you very much. Jeffrey L. Nauss MSI Training Programs (858) 799-5555 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121 From chemistry-request@server.ccl.net Fri Apr 7 17:23:12 2000 Received: from salve.edu (root@mail.salve.edu [208.131.51.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA17003 for ; Fri, 7 Apr 2000 17:23:11 -0400 Received: from salve5.salve.edu (salve5.salve.edu [208.131.51.7]) by salve.edu (8.9.3 (MessagingDirect 1.0.2)/8.9.3) with ESMTP id RAA28993; Fri, 7 Apr 2000 17:22:43 -0400 Date: Fri, 7 Apr 2000 17:15:05 -0400 (EDT) From: Ascanio DiPippo To: Peter Shenkin cc: chemistry@ccl.net Subject: Re: CCL:Comp Chem Lab Design In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Well put, Peter. I manufacture diabetic cough, cold and other pmedicinals. i tell my students to keep computational chemistry in proper perspective. You can't go to the drug store and by a floppy disk of cough syrup!! We're still chemists. Mix, heat, separate, purify, and analyze. :-) pacem in terris atque calcio. Ascanio On Fri, 7 Apr 2000, Peter Shenkin wrote: > > Dear All, > > > > I have the opportunity to design from scratch a new comp. chem. facility > > of about 50 sq. m. Our current layout is very basic - just desking > > against the walls. It would be nice to have something that created a > > more inspiring environment. > > Hi, > > How about hanging some test-tubes and beakers from the ceiling > to remind us of our ancient roots in physical reality? > > :-), > -P. > > On Fri, 7 Apr 2000, Charlie Laughton wrote: > > -- > ** Whether the playing field is level depends on the coordinate system. *** > ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* > *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > >