From D.Turner@sheffield.ac.uk Mon Jun 2 05:46:18 1997 Received: from pp2.shef.ac.uk for D.Turner@sheffield.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA20482; Mon, 2 Jun 1997 05:15:08 -0400 (EDT) Received: from ramsley.shef.ac.uk by pp2.shef.ac.uk with local SMTP (PP); Mon, 2 Jun 1997 10:14:55 +0100 Received: from RAMSLEY/MAILQUEUE by ramsley.shef.ac.uk (Mercury 1.21); 2 Jun 97 10:15:01 +0100 Received: from MAILQUEUE by RAMSLEY (Mercury 1.30); 2 Jun 97 10:14:42 +0100 From: "David B.Turner" To: zjhu@IRIS3.shmm.ac.cn (Zhengjian Hu) Date: Mon, 2 Jun 1997 10:14:38 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: PLS and GA source codes CC: chemistry@www.ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Message-ID: <64630391275@ramsley.shef.ac.uk> Hello There is some PLS source code (Fortran) available at http://dasher/wustl.edu. This code includes both the NIPALS and SIMPLS algorithms. This was written by Jay Ponder and Megan Fedders. As for GAs there are numerous sources; see, e.g., http://www.aic.nrl.navy.mil/galist or lancet.mit.edu:/pub/ga. Hope this helps Dave Turner > Date: Tue, 20 Dec 94 20:44:16 -0800 > From: zjhu@IRIS3.shmm.ac.cn (Zhengjian Hu) > To: chemistry@www.ccl.net > > > > From: zjhu@iris3.shmm.ac.cn > To: chemistry@www.ccl.net > > Dear CCL users, > > I have been trying to do some QSAR but I have no proper softwares. > I wonder if you could tell me how and where I can get the source code for > the following programs: > 1. Genetic algorithm > 2. Neural network > 3. Partial least squares > 4. Non-linear partial least squares > 5. Simulated annealing algorithm > > Thank you in advance!!! > > Hu Zengjian > > ------------------------------------------------------------------------ > Hu Zengjian (zjhu@iris3.shmm.ac.cn) > State Key Laboratory of Drug Research > Shanghai Institute of Materia Medica > Chinese Academy of Sciences > 294 Taiyuan Road, Shanghai 200031 > People's Republic of China > Tel. 86-21-64311833-615 > Fax. 86-21-64370269 > ------------------------------------------------------------------------- > > > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > Dr David B. Turner Dept. of Information Studies University of Sheffield, Sheffield S10 2TN UK Tel.: 0114 2222 679 Fax.: 0114 2780 300 E-mail: D.Turner@sheffield.ac.uk From aiba@c4-03.ethz.ch Mon Jun 2 06:46:18 1997 Received: from c4.ethz.ch for aiba@c4-03.ethz.ch by www.ccl.net (8.8.3/950822.1) id GAA20686; Mon, 2 Jun 1997 06:00:04 -0400 (EDT) From: Received: from c4-03-c4.ethz.ch by c4.ethz.ch (AIX 3.2/UCB 5.64/4.03) id AA23465; Mon, 2 Jun 1997 11:59:47 +0200 Received: by c4-03.ethz.ch (AIX 3.2/UCB 5.64/4.03) id AA02631; Mon, 2 Jun 1997 11:59:43 +0200 Date: Mon, 2 Jun 1997 11:59:43 +0200 Message-Id: <9706020959.AA02631@c4-03.ethz.ch> To: chemistry@www.ccl.net Subject: animation of presentation Dear Netters, Two questions: 1) Animation is desired for a talk which I am supposed to present some time in August. Hints will be greately appreciated about -- What software exists for animation of (graphical) data on Win95/NT platform and on Linux?! -- Is a laptop a must for such a presentation in sense of improving its quality and speed?! -- Any further general hints about hardware which is handy for preparation and for presentation.. -- Any hints about animation of molecular pictures (i.e. visualisation of mol.-orbitals), of motion of molecules, of animation of corresponding data (like energy and other observables - parallely in a separate window).. -- what is better - to use LCD or video or big computer screen? 2) Parallel question: to prepare a high-quality poster what will be the most convenient software (win95/NT and Linux)?! General remark. ^^^^^^^^^^^^^^^ Getting/purchasing hardware/software isn't a problem for our group. We are simply short of experience, time and relevant information. Thanks to all in advance, I believe the question is interesting, and there will be lots of responses. I will summarize with pleasure. Ayaz Bakasov. From arthur@csb0.IPC.PKU.EDU.CN Mon Jun 2 07:46:20 1997 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id HAA20939; Mon, 2 Jun 1997 07:27:23 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA27324; Mon, 2 Jun 97 19:25:57 -0700 Date: Mon, 2 Jun 1997 19:25:56 -0700 (PDT) From: Wang Arthur To: CCL mailing list Subject: Looking for compound models for CoMFA Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, We are looking for series of compounds which have been analyzed by CoMFA. These compounds will be used as CoMFA demonstration in a course for graduate students. We will appreciate it very much if you can offer the following: (1) The CoMFA analysis of this series of compounds should have been published. Please tell us the name of the journal, and the exact numbers of volume and pages. A copy of reprint will be better. (2) The coordinates of these compounds. They should have been properly superimposed. Better to be stored in SYBYL MOL2 format. Thank you in advance for your courtesy. Best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From pwalters@portal.vpharm.com Mon Jun 2 08:46:21 1997 Received: from portal.vpharm.com for pwalters@portal.vpharm.com by www.ccl.net (8.8.3/950822.1) id IAA21128; Mon, 2 Jun 1997 08:17:48 -0400 (EDT) Received: from neoprene.vpharm.com by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA24806; Mon, 2 Jun 1997 08:07:25 -0400 Sender: pwalters@portal.vpharm.com Message-Id: <3392BDC0.794B@portal.vpharm.com> Date: Mon, 02 Jun 1997 05:34:08 -0700 From: Pat Walters Organization: Vertex Pharmaceuticals X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Mime-Version: 1.0 To: Zhengjian Hu Cc: chemistry@www.ccl.net Subject: QSAR Packages Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Dear CCL users, > > I have been trying to do some QSAR but I have no proper softwares. > I wonder if you could tell me how and where I can get the source code for > the following programs: > 1. Genetic algorithm > 2. Neural network > 3. Partial least squares > 4. Non-linear partial least squares > 5. Simulated annealing algorithm An excellent free package is the QSAR program from Jay Ponder's group at Washington University in St. Louis. This program does Ordinary Least Squares, PLS, PCR, and it comes with source code. You can download QSAR from http://dasher.wustl.edu/ Have fun, Pat -- W. Patrick Walters, Ph.D. Staff Scientist, Computational Chemistry and Molecular Modeling Vertex Pharmaceuticals, Inc., 130 Waverley St., Cambridge, MA 02139 Voice: (617)577-6000 FAX: (617)577-6400 From brunob@helix.nih.gov Mon Jun 2 11:46:22 1997 Received: from mgcct6.nci.nih.gov for brunob@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id LAA22575; Mon, 2 Jun 1997 11:17:42 -0400 (EDT) Received: from mgcct6 (localhost [127.0.0.1]) by mgcct6.nci.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id NAA06911 for ; Mon, 2 Jun 1997 13:14:40 -0400 Sender: brunob@helix.nih.gov Message-ID: <3392FF80.794B@helix.nih.gov> Date: Mon, 02 Jun 1997 13:14:40 -0400 From: Bruno Bienfait Organization: National Cancer Institute X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: Computer Chemistry List Subject: Hexadecane/water partition coefficients: summary Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit A few weeks ago, I posted the following question: " I am looking for a program that can predict the hexadecane/water partition coefficients for organic molecules. Also, is there any database available containing exprimental values ? " Many thanks to people who replied. The programs are : AMSOL 5.4.1, QCPE 606 http://www.ccl.net/ccl/qcpe/QCPE/ent/e12/606.html http://www.chem.umn.edu http://www.psc.edu/general/software/packages/amsol/amsol.html Giesen, Storer, Cramer and Truhlar; J. Am. Chem. Soc. 1995, 117, 1057-1068. ASMOL 6.0, a commercial version distributed by Oxford Molecular (not available yet) http://pollux.chem.umn.edu/~amsol/ Spartan http://www.wavefun.com The new commercial version of AMPAC includes the solvatation model of AMSOL. Experimental values are available in the Medchem database from BioByte http://clogp.pomona.edu/medchem/chem/qsar-db/index.html Other experimental data : M. H. Abraham, G. S. Wittig, R. Fuchs, and E. J. Chambers. Thermodynamics of Solute Transfer from Water to Hexadecane. J. Chem. Soc. Perkin Trans. 2, 1990, 291-300. M. H. Abraham et al Journal of Pharmaceutical Sciences, Vol 83 (8), 1994, p 1085 Jian Li et al Anal. Chem. vol 65, 1993, p. 1443-1450 Leo, A. and Hansch, C, et al Chem. Review. 1971, 71, page 533 Bruno -- [ Bruno Bienfait, Ph. D. Laboratory of Medicinal Chemistry ] [ National Cancer Institute ] [ Email : brunob@helix.nih.gov National Institutes of Health ] [ Phone : (301) 402-3111 Building 37, Room 5B20 ] [ Fax : (301) 496-5839 Bethesda Maryland 20892 , USA ] [ WWW : http://schiele.organik.uni-erlangen.de/Bruno_Bienfait ]