From grzesb@asp.biogeo.uw.edu.pl Mon Jun 10 02:52:52 1996 Received: from asp.biogeo.uw.edu.pl for grzesb@asp.biogeo.uw.edu.pl by www.ccl.net (8.7.5/950822.1) id CAA07400; Mon, 10 Jun 1996 02:28:47 -0400 (EDT) Received: by asp.biogeo.uw.edu.pl (5.61/1.34) id AA15249; Mon, 10 Jun 96 08:32:57 +0200 Date: Mon, 10 Jun 96 08:32:57 +0200 From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Message-Id: <9606100632.AA15249@asp.biogeo.uw.edu.pl> To: chemistry@www.ccl.net Subject: correction: reading spectrums Dear Net, In my summary on creating color spectrums in InsightII I asked a new querry with mistake, that might be confusing! So, it should be: Does anybody know why insightII v.3.00 does NOT read spectrums created with InsightII v.95.0 ??? (InsightII v.3.00 of course can read spectrums created by itself [ and InsightII v.95.0 can read spectrums created by itself ] ) The question is why I cannot interchange spectrums from different versions ? Best regards Grzegorz Bakalarski,ICM From Vladimir.Shcherbukhin@hassle.se.astra.com Mon Jun 10 08:52:59 1996 Received: from x400.swip.net for Vladimir.Shcherbukhin@hassle.se.astra.com by www.ccl.net (8.7.5/950822.1) id HAA11091; Mon, 10 Jun 1996 07:58:21 -0400 (EDT) X400-Received: by /ADMD=INTERX/C=SE/; Relayed; Mon, 10 Jun 1996 13:58:02 +0200 X400-Received: by mta INTERX2 in /ADMD=INTERX/C=SE/; Relayed; Mon, 10 Jun 1996 13:58:02 +0200 X400-Received: by mta astrase1 in /ADMD=INTERX/C=SE/; Relayed; Mon, 10 Jun 1996 14:57:39 +0200 X400-Received: by /PRMD=ASTRA/ADMD=400NET/C=SE/; Relayed; Mon, 10 Jun 1996 14:58:19 +0200 Date: Mon, 10 Jun 1996 14:58:19 +0200 X400-Originator: Vladimir.Shcherbukhin@hassle.se.astra.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=ASTRA/ADMD=400NET/C=SE/;960610125819] Original-Encoded-Information-Types: teletex X400-Content-Type: P2-1984 (2) Content-Identifier: CSI NC V3.0 From: Shcherbukhin Vladimir Message-ID: <"001FE4A3.MAI*/G=Vladimir/S=Shcherbukhin/O=Astra Hassle AB/PRMD=ASTRA/ADMD=400NET/C=SE/"@MHS> To: CCL Subject: Summary: software for calculating solvent-accessible areas Hi folks, Many many thanks to everybody who has replied to the question which I recently posted on behalf of my colleague Marcel Linschoten. Some of you were interested in getting summary of replies, so here it is. Best regards, Vlad --------------------------------------------------------- Vladimir Scherbuhin (Ph.D.) ! phone: (+46-31)-776-2560 Precl. R&D, ASTRA Hassle AB ! FAX: (+46-31)-776-3710 Molndal S-43183, SWEDEN ! --------------------------------------------------------- internet: Vladimir.Shcherbukhin@Hassle.se.ASTRA.com --------------------------------------------------------- ======================================================== >Hello folks, >I'm looking for a program (may also include Sybyl SPL) to calculate >hydrophobic and hydrophilic areas on the solvent accessible surface of a >small >molecule. Who can help ? >Thanks, >Marcel Linschoten, Sweden ======================================================== Marcel: You might try HINT as it interfaces with Sybyl. It's available from EDUSOFT. See their web page for details: http://www.eslc.vabiotech.com/ --------------------------------------------------------- J. Bruce Pitner, Ph.D. pitner@bdrc.bd.com Becton Dickinson Research Center (919) 990-2147 P.O. Box 12016, RTP, NC 27709 Fax (919) 549-7572 --------------------------------------------------------- ========================================================= Hi, There is a program writen by P. Gaillard for Sybyl who calculate MLP and log P his name is Clip1.1. We are using it at the university of Namur and it seems it works well. If you are interested by thie program contact me. best regards, fred Ooms --------------------------------------- Ooms Frederic Faculte Universitaire Notre-Dame de la Paix Laboratoire de Chimie Moleculaire Structurale Rue de Bruxelles 61 B-5000 Namur (BELGIUM) Tel : 32(81) 724569 - Fax : 32(81) 724530 e-mail :ooms@scf.fundp.ac.be ========================================================= Hi Under SYBYL the best program to do that is an option Call Molcad. This program is able to display molecular properties on Connolly surfaces and Electron density surfaces. The only problem is that you need an SGI with 24 bitplanes and hardware Z bufferinstall. It is working well with an R4000 Indigo Elan Bye -- _____________________________________________________________________ ___________ Jacques-Antoine DURET GROUPE DE PHARMACOCHIMIE MOLECULAIRE UFR DE PHARMACIE Universite Joseph Fourier GRENOBLE 5 Avenue de Verdun Tel : (33) 76 04 10 00 38243 Meylan FRANCE Fax ; (33) 76 41 85 71 E-Mail : Jacques-Antoine.DURET@ujf-grenoble.fr _____________________________________________________________________ ========================================================= SAVOL2 is what you are looking for. I got it from Bob Pearlman at University of Texas, but it might be included with Sybyl. pearlman@vax.phr.utexas.edu. Yvonne Martin Abbott Laboratories ========================================================= Created, developed and extensively tested at the Institute of Medicinal Chemistry of the University of Lausanne , CLIP is a package with the following capabilities: Computation and representation of the Molecular Lipophilicity Potential (MLP) on the solvent-accessible surface of molecules and macromolecules; Calculation of n-octanol/water partition coefficients (log Poct) from the MLP on the solvent-accessible surface; Calculation of virtual log P values for individual conformers, and exploration of the lipophilicity range accessible to a compound; Computation and representation of the MLP in a given region of space around molecules and macromolecules; Computation and incorporation of the MLP into Comparative Molecular Field Analysis (CoMFA)?. Information about CLIP, publications can be found on the web at: http://www.unil.ch/pharm/clip/ -------------------------------------------------------------- Frederic Billois Universite de Lausanne Section de Pharmacie. Institut de Chimie Therapeutique. CH-1015 Dorigny-Lausanne Suisse Tel : +41.21.692.45.24 Fax : +41.21.692.45.05 e-mail : Frederic.Billois@ict.unil.ch WWW : http://www.unil.ch/pharm/ict/docs/ict.html ---------------------------------------------------------------- ========================================================= Dear Marcel: I have written an SPL script to calculate surface areas using the SAVOL program that is shipped with Sybyl 6.2. The script will also calculate per residue and per static set contributions to the surface area. If you define two statics sets, one for hydrophobic and another for hydrophilic atoms, my script should calculate exactly the quantities that you are interested in. The next e-mail message contains a copy of my SPL script. I hope you find it useful. Ciao, Konrad ------------------------------------------------------------------ | Konrad Koehler | Computational Chemistry Group | | internet: koehler@irbm.it | Department of Medicinal Chemistry | | | IRBM | | telephone: +39-6-910-93606 | Via Pontina Km. 30,600 | | fax: +39-6-910-93225 | 00040 Pomezia (Roma) | | | Italy | ------------------------------------------------------------------ ========================================================= Note: those of you who would like to get the SPL script, please send a message directly to Konrad Koehler. From gerwens@mbox.theochem.uni-hannover.de Mon Jun 10 10:52:58 1996 Received: from mgate.uni-hannover.de for gerwens@mbox.theochem.uni-hannover.de by www.ccl.net (8.7.5/950822.1) id KAA11765; Mon, 10 Jun 1996 10:04:41 -0400 (EDT) From: Received: from sun1.rrzn-user.uni-hannover.de (actually sun1.rrzn.uni-hannover.de) by mgate with SMTP (PP); Mon, 10 Jun 1996 16:04:12 +0200 Received: by sun1.rrzn-user.uni-hannover.de (SMI-8.6/SMI-SVR4) id QAA10010; Mon, 10 Jun 1996 16:03:52 +0200 Message-Id: <199606101403.QAA10010@sun1.rrzn-user.uni-hannover.de> Subject: Smallest rectangular Box of set of points? To: chemistry@www.ccl.net (CCL CCL) Date: Mon, 10 Jun 1996 16:03:49 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Dear CCL'ers, I've got the problem to find the smallest possible rectangular Box around a set of points (atoms) in space. Any suggestions or ideas are wellcome. I'll summerize the results. thanx in advance Heiko Gerwens Institut fuer Theoretische Chemie Universitaet Hannover Am Kleinen Felde 30 D-30167 Hannover Germany email: gerwens@mbox.uni.hannover.de From WILLSD@conrad.appstate.edu Mon Jun 10 13:52:58 1996 Received: from listserv.appstate.edu for WILLSD@conrad.appstate.edu by www.ccl.net (8.7.5/950822.1) id NAA13061; Mon, 10 Jun 1996 13:10:34 -0400 (EDT) Received: from spd.appstate.edu ([152.10.1.23]) by listserv.appstate.edu with ESMTP id <11244-6141>; Mon, 10 Jun 1996 13:10:32 -0500 Received: from conrad.appstate.edu by conrad.appstate.edu (PMDF V5.0-6 #8642) id <01I5QTMRUAHC9EDC51@conrad.appstate.edu> for CHEMISTRY@www.ccl.net; Mon, 10 Jun 1996 13:10:12 -0400 (EDT) Date: Mon, 10 Jun 1996 13:10:11 -0400 (EDT) From: willsd@conrad.appstate.edu Subject: mopac for NT? To: CHEMISTRY@www.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT I am contemplating porting the public domain version of mopac (either 6 or 7) to ms windows NT. Before doing so, I'd like to find out if anyone else may have already done this. The source code is available on the ccl archives, but the does not seem to be a NT exectable version there. So, does anybody out there have an NT version of MOPAC? Can anyone provide any hints about pitfalls I am likely to find in doing such a port? I assume that since the source code is freely available to the public, this is legal port to make, but if there is a difference of opinion about this, I'd like to hear about that as well. I will summarize to the list any information I get. Thanks, Steve Williams chemistry, asu willsd@appstate.edu From scho@quantum.cm.utexas.edu Mon Jun 10 14:53:00 1996 Received: from quantum for scho@quantum.cm.utexas.edu by www.ccl.net (8.7.5/950822.1) id OAA13406; Mon, 10 Jun 1996 14:09:36 -0400 (EDT) Received: by quantum (4.1/1.34/QUANTUM) id AA05503; Mon, 10 Jun 96 13:10:02 CDT From: scho@quantum.cm.utexas.edu (Sarah Schofield ) Message-Id: <9606101810.AA05503@quantum> Subject: Computing under SCO Unix To: chemistry@www.ccl.net Date: Mon, 10 Jun 1996 13:09:59 -0500 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Netters: Is anyone familiar with chemical computing under SCO Unix, a commercial Unix operating system for Intel (Pentium, etc) based machines? If so: 1) Is LINUX better? 2) Are a Fortran compiler, Mathematica, and TeX available for SCO Unix? 3) How does program operation compare with RISC based program operation? Thanks in advance for replies. scho@quantum.cm.utexas.edu From vuckovic@hyper.com Mon Jun 10 16:53:00 1996 Received: from www.hyper.com for vuckovic@hyper.com by www.ccl.net (8.7.5/950822.1) id QAA14005; Mon, 10 Jun 1996 16:09:30 -0400 (EDT) Received: from dragan2.hyper.com (dragan2.hyper.com [204.50.97.30]) by www.hyper.com (8.6.12/8.6.12) with SMTP id QAA01170 for ; Mon, 10 Jun 1996 16:20:04 -0400 Date: Mon, 10 Jun 1996 16:20:04 -0400 Message-Id: <199606102020.QAA01170@www.hyper.com> X-Sender: vuckovic@hyper.com X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====================_834448202==_" To: chemistry@www.ccl.net From: Dragan Vuckovic Subject: HyperChem User Group-II Announcement X-Attachments: C:\EUDORA\DRT2; --=====================_834448202==_ Content-Type: text/plain; charset="us-ascii" The First World HyperChem User Group Meeting - Second Announcement The Second announcement for HyperChem User Group Meeting (September 8-11, Clevelands House, Minett, Muskoka, Ontario, Canada) has been mailed. Interested persons should contact me or visit our home page (http://www.hyper.com, under the New section) for more information and the final registration form. --=====================_834448202==_ Content-Type: text/plain; charset="us-ascii" ********************************************************************* * Dr. Dragan Lj. Vuckovic phone: (519) 725-4040 * * International Marketing Manager fax: (519) 725-5193 * * Hypercube, Inc. e-mail: vuckovic@hyper.com * * 419 Phillip Street URL: http://www.hyper.com * * Waterloo, Ontario Info: info@hyper.com * * Canada, N2L 3X2 * ********************************************************************* --=====================_834448202==_-- From sxr224@anugpo.anu.edu.au Mon Jun 10 20:53:01 1996 Received: from anugpo.anu.edu.au for sxr224@anugpo.anu.edu.au by www.ccl.net (8.7.5/950822.1) id UAA15053; Mon, 10 Jun 1996 20:23:09 -0400 (EDT) Received: from surya.anu.edu.au (surya.anu.edu.au [150.203.193.135]) by anugpo.anu.edu.au (8.6.12/8.6.12) with SMTP id KAA26361; Tue, 11 Jun 1996 10:23:03 +1000 Message-Id: <199606110023.KAA26361@anugpo.anu.edu.au> Comments: Authenticated sender is From: "Shoba.Ranganathan" To: chemistry@www.ccl.net Date: Tue, 11 Jun 1996 10:01:04 +0000 Subject: CCL:SUMM:Homology Modelling question Reply-to: Shoba.Ranganathan@anu.edu.au CC: SIEW@vms.huji.ac.il, jane@nmrfam.wisc.edu, marsh@chet.medc.umn.edu Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) I would to thank all CCLers who responded to my request. Here's the summary for the "homology modelling" question (some answers are from bionet.xtallography while repeats and signatures were suppressed): > > I require references for the limits of homology > modelling, as well as the percentage of sequence > identity (in case I am unable to locate the reference). > ---------------------------------------------------------------------- From: treutlei@ludwig.edu.au Here is my favourite for this question: Sanders C and Schneider R. (1991) Database of Homology-Derived Protein Structures and the Structural Meaning of Sequence Alignment. Porteins: Struct., Funct., and Gen. 9, 56-68. Best regards, Herbert Treutlein +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: smb@bioch.ox.ac.uk You might want to consider using the term "comparative modelling", as opposed to "homology modelling". The reason for this is that the minimum sequence identity that is "required" for useful 3-D prediction and modelling can be as low as zero percent (or some other statistically insignificant similarity). Thus it is, in fact, possible to model the structure of a protein based on the structure of an unrelated (or very distantly related) protein. Check out the high quality structure prediction, which used a combination of several state-of-the-art techniques, in: ->TI: THE PROTEIN FOLD OF THE VON-WILLEBRAND-FACTOR TYPE-A DOMAIN IS PREDICTED TO BE SIMILAR TO THE OPEN TWISTED BETA-SHEET FLANKED BY ALPHA-HELICES FOUND IN HUMAN RAS-P21 AU: EDWARDS_YJK, PERKINS_SJ JN: FEBS LETTERS, 1995, Vol.358, No.3, pp.283-286 -- Simon M. Brocklehurst ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Aravind Mittur Chris Sander and Gert Vriend have written some very good reviews and articles on homology modeling over the last couple of years. You should perhaps read the Sanderss' group home page at http://www.embl-heidelberg.de. The cut-off depends on a number of factors, including functional validity. I can also recall an excellent review by Eisenhaber and others in Critical Reviews in Biochemistry and Molecular Biology early last year. Aravind M. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: crawfordoh@ornl.gov (Oakley H. Crawford) See S. Mosimann, R. Meleshko, and M. N. G. James, Proteins 23, No. 3, p. 301 (1995), and other papers in that issue of Proteins. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: wally@mag.com Our company, Molecular Applications Group (MAG), supports and markets a homology modeling package based on the work of our founder, Michael Levitt ["SegMod", J. Mol. Biol. 226, 507-533 (1992)]. It is a highly automated procedure, yet remarkably accurate. Our primary product, Look, acts as a graphical front-end to SegMod, permitting the user to focus on the most important part of the homology modeling process--the sequence alignment between your unknown and the reference structure--rather than the mechanics of building the homology model. For more information, please visit the following page on our Web site: In particular, please see MAG's validation study of SegMod: in which, for example, a homology model with an RMS error of 2.79 A for Calpha atoms was produced from a single template structure with only 27% sequence identity. Please contact me if you have further questions or would like to receive more information. Wally E. Reiher ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: Arne Elofsson According to Andrej Sali (and my memory) >50% identity, 90-95% of internal sidechain correclty predicted, rmsd >2 A 40-50% sequecnce identity 80% internal sidechain correclty predicted, rmsd 2.5 A 30-40% loops predicted wrongly, 75 % of internal sidechain not correctly predicted. arne ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: MARTIN@cmdb.pprd.abbott.com Jonathan Greer and colleagues have just written a chapter for Reviews in Computational Chemistry. He can be contacted at: Jonathan.Greer@abbott.com Yvonne Martin (I do not have a reply from Jonathan Greer till date - Shoba) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: schuller@indigo1.biomol.uci.edu (Dave Schuller) I assume you mean for SUCCESSFUL homology modeling? You can model anything you want; whether it is useful or meaningful is another question. I could point out a couple attempts that failed (in my view) with 18-20% identity. Some of the reasons for the failure: 1) despite the overall identity numbers, there was no homology at all for one of the regions modelled. 1b) This fact was obscured by incorrect sequence alignments. 2) The modelling attempts may have been influenced by an incomplete and incorrect crystal structure of a third homologous protein. Banci, Carloni & Savellini (1994) Biochemistry 33, 12356-12366. Smith, Du & Loew (1995) Nuclear Magnetic Resonanc of Paramagnetic Macromolecules, Kluwer Academic publishers, the Netherlands, pp. 75-93. naturally, the authors would probably prefer to dwell on the positive aspects, such as correct placement of some or all of the active site residues, and not on the fact that some residues were mis-placed by tens of Angstroms. Dave Schuller ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Homology modelling has been done with as little as 30% sequence identity to a known structural protein. Generally, one finds reports where there was ~40-50% sequence identity and 70% similarity via conservative replacements. -raman ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ =========================================================== 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 0200 Fax: +616-249-0415 Australia. email:Shoba.Ranganathan@anu.edu.au ===========(http://biocomp.anu.edu.au/~sra/)============== From axb224@anugpo.anu.edu.au Mon Jun 10 21:53:01 1996 Received: from anugpo.anu.edu.au for axb224@anugpo.anu.edu.au by www.ccl.net (8.7.5/950822.1) id VAA15246; Mon, 10 Jun 1996 21:34:25 -0400 (EDT) Received: from nicepc.anu.edu.au (nicepc.anu.edu.au [150.203.193.136]) by anugpo.anu.edu.au (8.6.12/8.6.12) with SMTP id LAA06248 for ; Tue, 11 Jun 1996 11:34:20 +1000 Message-Id: <199606110134.LAA06248@anugpo.anu.edu.au> Comments: Authenticated sender is From: "Andrey Blizniuk" Organization: ANU To: chemistry@www.ccl.net Date: Tue, 11 Jun 1996 10:57:21 +0010 Subject: Monter Carlo applications to diffusion? Reply-to: Andrey.Bliznyuk@anu.edu.au Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Dear CCLers, I am looking for application of Monter Carlo methods to the diffusion problem. Any references are welcome. It seems, people prefer to use Brownian dynamics (any ideas why?). Thanks, Dr. Andrey Bliznyuk Computational Molecular Biology and Drug Design Group Division of Molecular Biology and Biochemistry John Curtin School of Medical Research Australian National University PO Box 334, Canberra, ACT 2601 Australia Email: Andrey.Bliznyuk@anu.edu.au http://biocomp.anu.edu.au/~aab