From jkl@ccl.net Tue Sep 12 13:19:16 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA11327; Tue, 12 Sep 1995 13:19:14 -0400 Received: from bioc1.biosym.com for news@news.biosym.com by bedrock.ccl.net (8.6.10/950822.1) id NAA29401; Tue, 12 Sep 1995 13:19:11 -0400 Received: from news.biosym.com by bioc1.biosym.com (5.64/0.0) id AA27035; Tue, 12 Sep 95 10:19:31 -0700 Received: by news.biosym.com (4.1/SMI-4.1) id AA07851; Tue, 12 Sep 95 10:08:17 PDT Newsgroups: biosym.chemistry Path: iris158.biosym.com!cxl From: cxl@iris158.biosym.com (Congxin Liang) Subject: Flexible docking software Message-Id: <1995Sep12.170811.7799@biosym.com> Sender: news@biosym.com Nntp-Posting-Host: iris158 Organization: Biosym/MSI Distribution: biosym Date: Tue, 12 Sep 1995 17:08:11 GMT Apparently-To: CHEMISTRY@ccl.net Status: RO On Mon Sep 11 12:12:52 1995, Lim Teck Sin wrote: > It seems that many of the molecular docking packages only handle rigid >molecules. Anyone knows of any packages (public-domain or commerical or >yet-to-be-released-versions) that perform 'flexible' docking? In the 950 release from Biosym/MSI scheduled for next month, there is a new product named Affinity which does flexible docking. Both the ligand and receptor are flexible. It is an energy-based method and it combines the merits of Monte Carlo, minimization and dyanmics. It also uses the molecular mechanics/grid method of Luty et al. (JCC, 16, 454, 1995) to speed up the calculation and to include an implicit solvation model of Stouten et al. (Mol. Simulations, 10, 97, 1993). For more infomation, please contact your local Biosym/MSI sales office. Congxin Liang Biosym/MSI -- From jkl@ccl.net Wed Sep 13 01:15:41 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id BAA22444; Wed, 13 Sep 1995 01:08:35 -0400 Received: from sangam.ncst.ernet.in for niclai!root@iitm.ernet.in by bedrock.ccl.net (8.6.10/950822.1) id BAA04565; Wed, 13 Sep 1995 01:08:17 -0400 Received: from niclai.UUCP (uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id KAA21073 for chemistry@ccl.net; Wed, 13 Sep 1995 10:38:38 +0530 Received: from shiva.iitm.ernet.in by spark.iitm.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA24457; Wed, 13 Sep 95 10:23:58+060 Received: by shiva.iitm.ernet.in (5.57/Ultrix2.4-C) id AA18987; Wed, 13 Sep 95 09:32:37 EDT From: Superuser X-Mailer: SCO System V Mail (version 3.2) To: chem-comp@mailbase.ac.uk, chem-mod@mailbase.ac.uk, chemistry@ccl.net Date: Tue, 12 Sep 95 13:06:54 IST Message-Id: <9509121306.aa01763@niclai.niclai.ernet.in> Hello, I am looking for challenging placement opppurtunity anywhere in the world :-) please let me know if any one wants to hire me for their institution. You could reach me through email at: nachi@niclai.ernet.in I append a copy of my short CV for your ref Thanks, Balu. Curriculam - Vitae  NAME : S.BALASUBRAMANIAN AGE : 39-YEARS NATIONALITY : INDIAN ADDRESS : EDUCATION & TRAINING DIVISION (OFFICE) CENTRAL LEATHER RESEARCH INSTITUTE ADYAR.MADRAS-600 020.INDIA (RESIDENCE) : 7-EGMORE HIGH ROAD EGMORE.MADRAS-600 008.INDIA ACADEMIC QUALIFICATIONS : M.Sc.(ANALYTICAL & INORGANIC CHEMISTRY)-1977. Ph.D.(SYNTHETIC INORGANIC CHEMISTRY)-1985. FIELD OF SPECIALISATION : MACROCYCLIC COMPLEXES-PHOTO- & GALVANIC SYSTEMS-SPIN CROSSOVER AREA OF INTEREST COMPLEXES-MAGNETIC RESONANCE IMAGING-DEVELOPMENT OF NEW MATERIALS-SYSTEMS FOR MOCVD- PHOTOCHEMISTRY OF MACROCYCLIC COMPLEXES-NEW MINERAL TANNING AGENTS FOR LEATHER-INSTRUMENTAL TECHNIQUES FOR NOVEL APPLICATIONS- BIOMIMICS. EXPERIENCE : RESEARCH-TEACHING-OPERATION & MAINTENANCE OF SOPHISTICATED ANALYTICAL INSTRUMENTS. NUMBER OF PUBLICATIONS : THIRTY POSITION SOUGHT IN : ACADEMIC/INDUSTRIAL R&D/QUALITY CONTROL From jkl@ccl.net Wed Sep 13 05:45:45 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA24911; Wed, 13 Sep 1995 05:32:00 -0400 Received: from neumann.sissa.it for demaria@neumann.sissa.it by bedrock.ccl.net (8.6.10/950822.1) id FAA06168; Wed, 13 Sep 1995 05:31:50 -0400 Received: by neumann.sissa.it (AIX 3.2/UCB 5.64/4.03) id AA39666; Wed, 13 Sep 1995 11:30:16 +0200 From: demaria@neumann.sissa.it (Leonardo Demaria) Message-Id: <9509130930.AA39666@neumann.sissa.it> Subject: CNDO vibration frequencies. To: CHEMISTRY@ccl.net Date: Wed, 13 Sep 1995 11:30:15 +22311408 (DFT) Cc: demaria@neumann.sissa.it (Leonardo Demaria) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 736 Hi, does anyone knows where to find CNDO/1 and/or CNDO/2 vibration frequencies for any of these molecules: C2H2,C2H4,CH4,C2H6,C6H6 ? I'll summarize the answers. Ciao, -- Leonardo De Maria SISSA | Universita di Trieste Scuola Internazionale | Dipartimento di Fisica Teorica Superiore di Studi Avanzati | Strada Costiera 11 via Beirut 2-4, Grignano | Miramare-Grignano I-34014 - Trieste | I-34014 - Trieste tel: +39 40 3787506 | tel: +39 40 224265 fax: 3787528 | fax: 224601 e-mail:demaria@neumann.sissa.it | e-mail : demaria@vstst0.ts.infn.it From nauss@ucmod2.che.uc.EDU Wed Sep 13 08:45:47 1995 Received: from phem3 for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.10/950822.1) id IAA26599; Wed, 13 Sep 1995 08:39:34 -0400 Received: from UCBEH.SAN.UC.EDU (SMTPUSER@UCBEH) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HV7Z7GJNZ48Y76A3@phem3.acs.ohio-state.edu>; Wed, 13 Sep 1995 08:39:25 EDT Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-4 #7238) id <01HV7Z6BL1KC03R6I9@UCBEH.SAN.UC.EDU>; Wed, 13 Sep 1995 08:38:36 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:toukie@zui.unizh.ch id AA27175; Wed, 13 Sep 1995 08:45:11 -0400 Date: Wed, 13 Sep 1995 08:45:11 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Re: PROBE? To: toukie@zui.unizh.ch Cc: chemistry@www.ccl.net Reply-to: nauss@ucmod2.che.uc.EDU Message-id: <9509131245.AA27175@ucmod2.che.uc.EDU> Content-transfer-encoding: 7BIT >From toukie@zui.unizh.ch Wed Sep 13 04:30:13 1995 > I have never heard of the programme PROBE. Could you please advise me >what this programme is supposed to do? There may be others in a similar situation so here is what I got. PROBE is a compuer program employing an integrated neural network approach to protein structure prediction. It relates the amino acid sequence of a protein to features of its secondary and tertiary structure. Then, I got this from Edward C. Hauer: From hauer@ftdetrck-ccmail.army.mil Mon Sep 11 14:10:50 1995 This is all I have. 1 AU - Holbrook SR AU - Dubchak I AU - Kim SH TI - PROBE: a computer program employing an integrated neural network approach to protein structure prediction MH - Amino Acid Sequence MH - Molecular Sequence Data MH - Neural Networks Computer MH - Protein Structure,Secondary MH - Software MH - Program PROBE MH - Computers MH - neural networks MH - Proteins MH - Amino Acids MH - Disulfides MH - secondary structure AB - A computer program, PROBE, has been designed for the prediction of protein structural features from amino acid sequence. This program integrates a variety of computer-simulated neural networks, each predicting an aspect of protein structure, into a single, easy-to-use package. The surface accessibility of each residue, the presence of disulfide bonds, the overall secondary structure composition and the residue secondary structures, including beta-turn type, are predicted. In addition, the overall amino acid composition and relative hydrophobicity are used to determine whether a protein belongs to one of four common folding motifs. PROBE is able to compare and synergistically improve the predictions by allowing communication between the different networks SO - Biotechniques 1993;14:984-989 So there is a literature reference for it. But we do not get that journal here. Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC http://www.che.uc.edu/~nauss * **************************************************************************** From antunez@chem.cinvestav.mx Wed Sep 13 11:00:50 1995 Received: from latina.chem.cinvestav.mx for antunez@chem.cinvestav.mx by www.ccl.net (8.6.10/950822.1) id KAA29272; Wed, 13 Sep 1995 10:50:18 -0400 Received: by latina.chem.cinvestav.mx (5.x/SMI-SVR4) id AA07187; Wed, 13 Sep 1995 08:47:52 -0600 Date: Wed, 13 Sep 1995 08:47:51 -0600 (CST) From: Sandra Antunez To: CHEMISTRY@www.ccl.net Subject: Re: PLOTMTV (fwd) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Tue, 12 Sep 95 17:42:54 PDT From: ktoh@td2cad.intel.com To: Mariusz.Klobukowski@ualberta.ca, antunez@chem.cinvestav.mx, pelleque@scripps.edu Subject: Re: PLOTMTV Hmmm, I seem to be very popular on the CCL today :-) But could someone tell me what CCL stands for? Anyway, here's the information you requested on plotmtv. Plotmtv is available from ftp.x.org (see details below) and is in the public domain. Feel free to repost this to the CCL mailing list. Kenny Toh --------------------------------------------------------------- OVERVIEW -------- PLOTMTV is a multipurpose X11 plotting program. PLOTMTV specializes in contour plots, but it can also handle 2D and 3D plots. The plot-types supported are as follows: * contour plots (rectangular grid, as well as triangular mesh) * 2D line and scatter plots (x-vs-y) * 3D surface , line and scatter plots * vector plots * probability plots * histograms * barcharts The program has an rough but functional Graphical User Interface, through which it is possible to zoom in, zoom out, pan, toggle between 2D and 3D plots, and rotate 3D plots. Both color and grayscale postscript output are supported. PLOTMTV V1.4.1 is available on the following sites: ftp.x.org: /contrib/applications/Plotmtv1.4.1.tar.Z. The program has been compiled on IBM RS6000, Sun SPARC, as well as HP700 workstations. The X11 routines use the X11R4 Xlib library, but the program has reportedly been compiled successfully on X11R5. PLOTMTV is based on the DRAWPLOT, CONTOUR and PDRAW programs from U.C. Berkeley (yes, I'm responsible for those too!). PLOTMTV essentially combines all the capabilities of the three packages into one single package. AUTHOR INFO ----------- Written by Kenny Toh (ktoh@td2cad.intel.com), software developer for the Technology CAD Department, Intel Corp, Santa Clara. If you like this software, send me a note... STANDARD DISCLAIMER ------------------- # # Permission to use, copy, modify, and distribute this software and its # documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies and that # both that copyright notice and this permission notice appear in # supporting documentation. # # These software is provided AS IS with no warranties of any kind. The author # shall have no liability with respect to the infringement of copyrights, # trade secrets or any patents by these file or any part thereof. In no # event will the author be liable for any lost revenue or profits or # other special, indirect and consequential damages. # # From mac@metis.tripos.com Wed Sep 13 11:15:50 1995 Received: from gatekeeper.tripos.com for mac@metis.tripos.com by www.ccl.net (8.6.10/950822.1) id LAA29651; Wed, 13 Sep 1995 11:08:11 -0400 Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id KAA03335; Wed, 13 Sep 1995 10:06:56 -0500 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma003333; Wed Sep 13 10:06:47 1995 Received: from metis.UUCP (metis.tripos.com [192.160.145.41]) by tripos.tripos.com (8.6.12/8.6.12) with SMTP id KAA14399; Wed, 13 Sep 1995 10:03:59 -0500 Received: by metis.UUCP (4.0/4.7) id AA06516; Wed, 13 Sep 95 08:03:52 PDT Message-Id: <9509131503.AA06516@metis.UUCP> To: nauss@ucmod2.che.uc.EDU Cc: chemistry@www.ccl.net, DIBUG@COMP.BIOZ.UNIBAS.CH Subject: Re: CCL:Phi-Psi plots In-Reply-To: Your message of Mon, 11 Sep 95 16:43:47 -0400. <9509112043.AA08047@ucmod2.che.uc.EDU> Date: Wed, 13 Sep 95 10:03:52 EDT From: "Malcolm A. Cline" Do you have SYBYL available? You can use the Molecular Spreadsheet to plot data of this type, even if it comes from external programs. Graph axes and ranges can be specified. There is even a built-in option for angle ranges (0-360 or -180 to 180). If you also have the Biopolymer module, the RAMACHANDRAN command works on conformational torsions of ANY type of biopolymer (protein, DNA, RNA, sugars). The axis ranges are automatically set to -180 to 180 and are not truncated. mac Malcolm A. Cline Tripos, Inc. From jkl@ccl.net Wed Sep 13 12:45:50 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA01853; Wed, 13 Sep 1995 12:37:59 -0400 Received: from admaxp.unca.edu for JAMES@unca.edu by bedrock.ccl.net (8.6.10/950822.1) id MAA09335; Wed, 13 Sep 1995 12:37:57 -0400 Received: from cluster.unca.edu by cluster.unca.edu (PMDF V5.0-4 #5911) id <01HV8745O9BK8WWMTC@cluster.unca.edu> for CHEMISTRY@ccl.net; Wed, 13 Sep 1995 12:37:12 -0400 (EDT) Date: Wed, 13 Sep 1995 12:37:11 -0400 (EDT) From: "Charles G. James" Subject: Frugal Chemist's Software Symposium call for papers. To: CHEMISTRY@ccl.net Message-id: <01HV8745PBWI8WWMTC@cluster.unca.edu> Organization: University of North Carolina at Asheville X-VMS-To: IN%"CHEMISTRY@ccl.net " MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT A Frugal Chemist's Software Symposium will be held by the Computers in Chemistry (COMP) Division of the American Chemical Society at the Spring Meeting, New Orleans, March 24-29 1996. Frugal is defined as: avoiding unnecessary expenditure of money, thrifty, costing little, inexpensive. The symposium will focus on using different software to do research or teach chemistry on a budget. Presentations are invited about software or applications of existing software which have been used to accomplish a chemist's goals when money is limited. A title, and short abstract is needed by November 1st, 1995. Send abstracts and questions to: Dr. Charles G. James, Jr. Dept. of Chemistry, University of North Carolina at Asheville Asheville, NC 28804-3299, USA, VOICE: (704)251-6443 FAX: (704)251-6041 E-mail: james@unca.edu From bear@ellington.pharm.arizona.edu Wed Sep 13 15:15:52 1995 Received: from ellington.pharm.arizona.edu for bear@ellington.pharm.arizona.edu by www.ccl.net (8.6.10/950822.1) id PAA05647; Wed, 13 Sep 1995 15:12:15 -0400 Received: by ellington.pharm.arizona.edu (950215.SGI.8.6.10/920502.SGI) id MAA07349; Wed, 13 Sep 1995 12:08:36 -0700 Date: Wed, 13 Sep 1995 12:08:36 -0700 From: bear@ellington.pharm.arizona.edu (Soaring Bear) Message-Id: <199509131908.MAA07349@ellington.pharm.arizona.edu> To: chemistry@www.ccl.net Subject: Biosym's Apex QSAR Questions Cc: bear@ellington.pharm.arizona.edu Howdy fellow comp-chemers: Since there appears to be very few users of Biosym's Apex QSAR module, I would like to get in touch with anyone who has ever used it. Since Biosym's help center is out to lunch with its merger and the Dibug listserve crashed 2 weeks ago when someone's message repeated 20 time, I'm compelled to ask this broader group some software specific questions. 1) I've built an Apex knowledge base from 5 dozen analogs, each with around half dozen conformers, each with ED50 and LD50. Build takes all night and indicates many hundreds of biophores. I understand filters can get rid of the worst. I need more help than the Apex manual and tutorial gave in reasoning out what adjustments to make first in filtering, properties & sites to narrow things down further. I realize this is a fairly broad question but it is only slightly touched on in the manual on pg 5-29. I hope some real experiences will clarify this. 2) The secondary site choices don't make much sense (and of course there's no explaination in the manual). For examples: -steric 'presence' makes plenty of sense, but what sense is steric 'hydrophobicity' when there is a seperate hydrophobicity presence available? -H-acceptor 'presence' makes sense but what is H-acceptor 'donor' when there is a seperate H-donor 'presence' selection available? 3) Pursuing this line, what is the difference between biophore refractivity, global refractivity, hydrophobic refractivity, steric refractivity.....? 4) I would be very interested in what task parameters and activity classes others have used (task.TST) I appreciate any help or suggestions you might have about this. thankyou, Soaring Bear _____ ____ bear@ellington.pharm.arizona.edu * ___) * _ \ http://ellington.pharm.arizona.edu/~bear : (___ : |_) : Cyber-Chemist: cancer drug design topo-O O-topo \___ \ | _ < Molecular & Nutritional Biochemist 5'. : : .*** ___) : | |_) : Herbs, Nutrition, Natural Dentistry |'*. .*'| | (_____/oaring |____/ear, UA New Pharmacy 404, Tucson 85721 | | *.,* | | | 3'*,DNA helix| *' '***' '**' From jkl@ccl.net Wed Sep 13 15:30:52 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id PAA05798; Wed, 13 Sep 1995 15:18:47 -0400 Received: from crash.cts.com for surles@intsim.com by bedrock.ccl.net (8.6.10/950822.1) id PAA11122; Wed, 13 Sep 1995 15:18:42 -0400 Received: from [198.68.169.77] by crash.cts.com with smtp (Smail3.1.29.1 #5) id m0ssxK5-0001uiC; Wed, 13 Sep 95 12:18 PDT Message-Id: X-Sender: surles@crash.cts.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 13 Sep 1995 12:21:57 -0800 To: Lim Teck Sin From: surles@intsim.com (Mark C. Surles) Subject: Re: CCL:Flexible docking software Cc: chemistry@ccl.net > It seems that many of the molecular docking packages only handle rigid >molecules. Anyone knows of any packages (public-domain or commerical or >yet-to-be-released-versions) that perform 'flexible' docking? > Thanks. > >best regards - teck-sin Sculpt from Interactive Simulations provides both flexible receptor and ligand during real-time, user-guided docking. Flexibility is a function of energy minimization. See the Flavin/Flavodoxin, HIV protease, and Beta lactamase examples in the demos. Demos are available via the WWW at http://www.intsim.com/~isigen or send email to intsim-support@intsim.com. Mark Surles Interactive Simulations, Inc. Phone: (619) 658-9462 5330 Carroll Canyon Road FAX: (619) 658-9463 Suite 203 Email: surles@intsim.com San Diego, CA 92121 URL: http://www.intsim.com/~isigen From jkl@ccl.net Wed Sep 13 18:15:55 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA08931; Wed, 13 Sep 1995 18:15:09 -0400 Received: from gatekeeper.es.dupont.com for hodgecn@chemsci5.dmpc.com by bedrock.ccl.net (8.6.10/950822.1) id SAA12755; Wed, 13 Sep 1995 18:15:07 -0400 Received: by gatekeeper.es.dupont.com; id AA08619; Wed, 13 Sep 95 18:15:06 -0400 Received: from [158.117.153.78] (esm153078) by chemsci5.dmpc.com (5.0/SMI-SVR4) id AA03200; Wed, 13 Sep 1995 18:12:51 -0400 Date: Wed, 13 Sep 1995 18:12:49 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Organization: The DuPont Merck Pharmaceutical Company X-Mailer: Eudora 1.5.1 for Macintosh To: chemistry@ccl.net From: hodgecn@chemsci5.dmpc.com (Nick Hodge) Subject: Re: CCL:Flexible docking software Content-Length: 3185 A brief expansion on Congxin's note regarding flexible docking (appended below): As indicated, the method was developed at DuPont Merck and employs molecular dynamics to 'fly' a ligand into the active site of an enzyme. The active site is flexible and represented explicitly, an intermediate region of the enzyme is restrained, and a grid represents the rest of the enzyme. An atom-based solvation term is added (Stouten et al. Mol. Simulations, 10, 97, 1993). The initial implementation (Luty et al., JCC, 16, 454, 1995) was able to reproduce the crystallographic orientation of benzamidine in trypsin rapidly and accurately, starting from random orientations outside of the active site; similarly, leucine hydroxamic acid finds its way into the crystallographically observed orientation in thermolysin (Wasserman and Hodge, Proteins: Structure, Function and Genetics, in press). In neither case do we attempt to correlate energies with the experimentally observed conformations, but preliminary analysis suggests that some correlation is possible. The successful extension to thermolysin and a more flexible inhibitor is also encouraging. However, the method has to be considered preliminary and in need of extensive testing and improvement. The Biosym implementation includes a Monte Carlo conformation/location generator and minimization to find optimum docked sites, as well the Discover 3.0 environment and cvff or cff91 forcefields; Amber is still being used as well at DuPont Merck. The results with cvff are similar, although not identical, to Amber in the limited comparisons that have been run. We are very interested in comments, suggestions, enhancements etc. to the method. We should also make clear that it is an extension of earlier and continuing docking protocols of Goodford, Olson, Kuntz, Bohm etc. and relies on many of their observations and ideas. Nick Hodge DuPont Merck At 3:55 AM 9/13/95, Congxin Liang (cxl@iris158.biosym.com) wrote: >On Mon Sep 11 12:12:52 1995, Lim Teck Sin wrote: > >> It seems that many of the molecular docking packages only handle rigid >>molecules. Anyone knows of any packages (public-domain or commerical or >>yet-to-be-released-versions) that perform 'flexible' docking? > >In the 950 release from Biosym/MSI scheduled for next month, >there is a new product named Affinity which does flexible docking. >Both the ligand and receptor are flexible. It is an energy-based >method and it combines the merits of Monte Carlo, minimization and dyanmics. >It also uses the molecular mechanics/grid method of Luty et al. >(JCC, 16, 454, 1995) to speed up the calculation and to include >an implicit solvation model of Stouten et al. (Mol. Simulations, >10, 97, 1993). For more infomation, please contact your local >Biosym/MSI sales office. > >Congxin Liang >Biosym/MSI -- C. Nick Hodge, Ph.D. Head, Computer Aided Drug Design Group The DuPont Merck Pharmaceutical Company P.O. Box 80353, Wilmington, DE 19880-0353 Phone: +1 (302) 695 3698 Fax: +1 (302) 695 2813 Internet: hodgecn@chemsci5.dmpc.com Please note the new address (chemsci5) as chemsci1 will not work after August 7th. From sxr224@anugpo.anu.edu.au Wed Sep 13 21:30:57 1995 Received: from anugpo.anu.edu.au for sxr224@anugpo.anu.edu.au by www.ccl.net (8.6.10/950822.1) id VAA10507; Wed, 13 Sep 1995 21:16:34 -0400 Received: from surya.anu.edu.au (surya.anu.edu.au [150.203.7.194]) by anugpo.anu.edu.au (8.6.12/8.6.12) with SMTP id LAA26586 for ; Thu, 14 Sep 1995 11:16:19 +1000 Message-Id: <199509140116.LAA26586@anugpo.anu.edu.au> Comments: Authenticated sender is From: "Shoba Ranganathan" To: chemistry@www.ccl.net Date: Thu, 14 Sep 1995 11:12:53 +0000 Subject: CCL:PROBE? Reply-to: Shoba.Ranganathan@anu.edu.au Priority: normal X-mailer: Pegasus Mail for Windows (v2.0-WB3) Jeff Nauss writes: > > AU - Holbrook SR > AU - Dubchak I > AU - Kim SH > TI - PROBE: a computer program employing an integrated neural network > approach to protein structure prediction > SO - Biotechniques 1993;14:984-989 > > So there is a literature reference for it. But we do not get that > journal here. > I have a copy of the article - but the program can only predict tertiary structures for four protein folds: 1. 4-helical bundle, 2. TIM barrel, 3. Rossmann fold (nucleotide binding domain) and 4. immunoglobin fold. So if one of these 4 folds are suspected, PROBE is the way to go. Nominal fee for academic and non-profit users. Contact: otl@violet.berkeley.edu (for licensing) or srholbrook@lbl.bitnet (these e.mail addresses are from the 1993 publication and may be outdated). Just my A$0.02 worth (~US$0.0175!) Shoba =========================================================== Dr. Shoba RANGANATHAN Computational Mol Biology & Drug Design Group Div. of Biochemistry & Mol. Biology John Curtin School of Medical Research Australian National University Tel: +616-279-8301 Canberra ACT 2002 Fax: +616-249-0415 Australia. email:Shoba.Ranganathan@anu.edu.au ----------------------------------------------------------