From lchirlia@cc.brynmawr.edu Tue May 24 09:41:39 1994 Received: from cc.brynmawr.edu for lchirlia@cc.brynmawr.edu by www.ccl.net (8.6.4/930601.1506) id JAA02598; Tue, 24 May 1994 09:34:33 -0400 Received: by cc.brynmawr.edu (5.57/cc09-01-92) id AA10146; Tue, 24 May 94 09:37:40 -0400 Message-Id: <9405241337.AA10146@cc.brynmawr.edu> Subject: SUMMARY:protein structure det. and docking To: chemistry@ccl.net Date: Tue, 24 May 94 9:37:40 EDT From: Lisa Emily Chirlian X-Mailer: ELM [version 2.3 PL11] I posted: > > I am interested in hearing peoples opinions on any > commercially available (or public domain) software for protein > structure determination and docking. Please e-mail, I will summarize > for anyone interested. Most of the responses I got were from people requesting the summary. Several people recommended different packages, no package was mentioned more than once. Thanks to everyone who responded. The software mentioned was: DOCK I.D. Kuntz UCSF MidasPlus T. Ferrin UCSF SPARTAN Wavefunction Inc. FLIMMSY" N. Richards U. of Florida SYBYL Tripos DGEOM QCPE CHARMm MSI QUANTA MSI INSIGHT Biosym ------------------------------------------------------------------------------- Lisa Chirlian lchirlia@cc.brynmawr.edu Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA 19010 ------------------------------------------------------------------------------- From windemut@cumbnd.bioc.columbia.edu Tue May 24 11:42:05 1994 Received: from cumbnd.bioc.columbia.edu for windemut@cumbnd.bioc.columbia.edu by www.ccl.net (8.6.4/930601.1506) id KAA03333; Tue, 24 May 1994 10:44:02 -0400 Received: from sirius by cumbnd.bioc.columbia.edu (NX5.67d/NX3.0M) id AA29963; Tue, 24 May 94 10:43:50 -0400 From: Andreas Windemuth Message-Id: <9405241443.AA29963@cumbnd.bioc.columbia.edu> Received: by sirius.bioc.columbia.edu (NX5.67d/NX3.0X) id AA12862; Tue, 24 May 94 10:43:52 -0400 Date: Tue, 24 May 94 10:43:52 -0400 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry@ccl.net Subject: Re: SUN vs HP workstations Cc: windemut@cumbnd.bioc.columbia.edu > First of all you may take into account usual benchmarks data as > SPECint, SPECfp and LINPACK MFLOPS. There are: > workstation SPECint92 SPECfp92 > HP9000 712/60 58 79 > SUNstation 20 mdl 50 69,2 78,3 > > It might be worth noting that the 712/80 (80MHz PA-1.1) is rated by HP at the same SPECfp92 as the 712/60 (60MHz PA-1.1). There has been evidence that this (quite improbable) result was achieved by intentionally slowing the benchmarks for the faster machine, in order to protect the more expensive 7?5 line of technical workstations. Indeed, when we run MD on our 712/80, we find that its performance is more consistent with a SPECfp92 rating of above 100, just what you would expect by simple clock rate extrapolation of either the 735 or the 712/60. >From my experience, HP is faster than anything else on the market, and they are pretty nice machines, too. --- Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Department of Biochemistry and Biophysics |630 West 168th St. BB-221 | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut@cumbnd.bioc.columbia.edu +-------------------------------------------------------------------- I have no affiliation with HP and speak for nobody but myself. From adnrdz@dec1.ifisica.uaslp.mx Tue May 24 16:40:58 1994 Received: from dec1.ifisica.uaslp.mx for adnrdz@dec1.ifisica.uaslp.mx by www.ccl.net (8.6.4/930601.1506) id QAA07311; Tue, 24 May 1994 16:08:06 -0400 Received: by dec1.ifisica.uaslp.mx (5.57/Ultrix3.0-C) id AA03742; Tue, 24 May 94 16:13:49 -0400 Date: Tue, 24 May 94 16:13:49 -0400 From: adnrdz@dec1.ifisica.uaslp.mx (Prof. Adan Ruben Rodriguez Dominguez) Message-Id: <9405242013.AA03742@dec1.ifisica.uaslp.mx> To: chemistry@ccl.net Subject: Second Mathematica Congress ***********************Second International****************** *********************** Congress on ****************** *********************** Mathematica as an ****************** ***************** Educational and Research Tool ************* August 22-26, 1994 Universidad Autonoma de San Luis Potosi, San Luis Potosi, Mexico. PROGRAM: The aim is to bring together scientists and teachers >from a wide variety of fields to discussing experiences related to the mathematical software in the classroom or in research. There will be plenary sessions of invited papers (1 hour), and also short papers. LOCATION: San Luis Potosi is an old colonial town with excellent restaurants. The seminar will take place at the five star hotel Quinta Real. Lodging for one week is $320. Because of its high elevation, San Luis Potosi has a mild climate even in August. You can fly to San Luis Potosi either through Mexico City, or through San Antonio. CALL FOR PAPERS: Titles and abstracts of contributed papers must be last received by july 15, 1994. The abstracts may be submitted in either Spanish or English not to exceed one page, preferably by e-mail. INFORMATION: Organizing Committee CMEI-II, Dra. Lilia del Riego, Facultad de Ciencias-UASLP, Zona Universitaria, Diagonal Sur, 78290 Mexico. Tels. 52(48)175251, Fax 52(48)130871, e-mail: lilia@dec1.ifisica.uaslp.mx, or Dr. Adan Ruben Rodriguez D, Instituto de Fisica-UASLP, Tels. 52(48)137557,178299 ext 28, Fax 52(48)133874, e-mail: adnrdz@dec1.ifisica.uaslp.mx. **********************Invited Speakers *********************** L. Cruz Kuri, Universidad de Veracruz, Mexico, CTJ Dodson, Toronto University, Canada, Marisa Fernandez, Universidad del Pais Vasco, Spain Alfred Gray, University of Maryland, USA M. Mezzino, University of Houston-Clear Lake, USA Ben Friedman, Wolfram Research **********************5 Day Workshop on Mathematica************* given by A. Gray, M. Mezzino and CTJ Dodson, DCM Burbulla and M. Pinsky Beginner's, Intermediate and Advanced Level. ***************************************************************** From C1790@SLVAXA.UMSL.EDU Tue May 24 18:42:25 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.4/930601.1506) id SAA09072; Tue, 24 May 1994 18:07:25 -0400 From: Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.2-11 #2503) id <01HCQ41S0GNKCWH646@SLVAXA.UMSL.EDU>; Tue, 24 May 1994 17:10:03 CST Date: Tue, 24 May 1994 17:10:03 -0600 (CST) Subject: PROGRAM TO CALCULATE LOG(P) To: CHEMISTRY@ccl.net Message-id: <01HCQ41S1SW2CWH646@SLVAXA.UMSL.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT DEAR NETTERS, I'M LOOKING FOR A PROGRAM THAT WILL CALCULATE (PREDICT) THE LOG(P) OF PROTEINS AND OF ORGANIC COMPOUNDS. I WANT TO ESTIMATE THE HYDROPHOBIC/ HYDROPHILIC INDEX FOR A SERIES OF THESE COMPOUNDS. CAN ANYONE SUGGEST ANY PROGRAMS? THANKS ... BILL WELSH DEPT. OF CHEMISTRY UNIV. OF MISSOURI-ST. LOUIS From tudor@wucmd.wustl.edu Tue May 24 19:40:55 1994 Received: from wugate.wustl.edu for tudor@wucmd.wustl.edu by www.ccl.net (8.6.4/930601.1506) id TAA09421; Tue, 24 May 1994 19:23:36 -0400 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA19015; Tue, 24 May 1994 18:23:35 -0500 Received: by wucmd (920330.SGI/911001.SGI) for @wugate.wustl.edu:CHEMISTRY@ccl.net id AA08671; Tue, 24 May 94 16:42:45 -0500 Date: Tue, 24 May 1994 16:41:03 -0500 (CDT) From: Tudor Oprea Sender: Tudor Oprea Reply-To: Tudor Oprea Subject: Re: CCL:PROGRAM TO CALCULATE LOG(P) To: C1790@SLVAXA.UMSL.EDU Cc: CHEMISTRY@ccl.net In-Reply-To: <01HCQ41S1SW2CWH646@SLVAXA.UMSL.EDU> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Bill, If you have either Sybyl, Insight II or Chem-X, then you should get HINT! 2.0 - available from EduSoft (Ashland, VA). E-mail gkellogg@gems.vcu.edu. The program was developed by Glen Kellogg and Donald Abraham - see J Comput Aided Mol Design 5 (1991) 545-552, and the 2.0 version includes a HintLogP estimation. This is an aftermarket product sold independently for users of the above programs. The Insight version is interfaced with Daylight Toolkit. For PC users (also available for workstations), you can get PCModels, available >from Daylight CIS (Santa Fe, NM). Contact Yosef Taitz (yosi@daylight.com) for details. The newest version of CLogP is CLogP3, which is included in PCModels. This is also marketed by Biobyte (Claremont, CA), and is authored by Albert Leo and David Weininger. Both EduSoft and Daylight offer substantial discounts for academic users. Hope this helps. Tudor ========================== Tudor-Ionel Oprea = Tel. (1-314) 935 4672 = Research Associate = Fax. (1-314) 935 4979 = Washington University Center for Molecular Design = Email: = Lopata 510, Box 1099, One Brookings Drive = tudor@wucmd.wustl.edu = St.Louis MO 63130 ==========================