From P.C.H.Mitchell@reading.ac.uk Mon Mar 13 06:12:16 1995 Received: from sums1.rdg.ac.uk for P.C.H.Mitchell@reading.ac.uk by www.ccl.net (8.6.10/930601.1506) id FAA12383; Mon, 13 Mar 1995 05:41:21 -0500 Received: from scsscsc1 (actually host scsscsc1.rdg.ac.uk) by sums1.rdg.ac.uk with SMTP - Local (PP); Mon, 13 Mar 1995 10:39:53 +0000 Date: Mon, 13 Mar 1995 10:39:36 +0000 (GMT) From: Philip Mitchell To: FOX Cc: chemistry@ccl.net, FOX@cmchem.chem.cmu.edu, Peter Wolohan , Dr John Upham Subject: Re: CCL:Gaussian 94 workshop, June 6-9, Erlangen Germany In-Reply-To: <950310075536.30e02bb2@cmchem.chem.cmu.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Please send details - Dr Philip C.H. Mitchell Mail: Department of Chemistry, University of Reading, Whiteknights, Reading RG6 2AD, UK Email(JANET): scsmitch@reading.ac.uk or: P.C.H.Mitchell@reading.ac.uk Voice: +44 (0)734 875123 x7448 or x6591 (secretary) Fax: +44 (0)734 311610 On Fri, 10 Mar 1995, FOX wrote: > > INTRODUCTION TO GAUSSIAN 94: THEORY AND PRACTICE > > Date: June 6-9, 1995 > > Location: CCC Erlangen, Germany > Cost: $250.00 U.S. > Contact: Workshop coordinator at Gaussian, Inc. > FAX: (412)279-2118 > E-mail: info@gaussian.com > > The CCC is pleased to host "Introduction to Gaussian 94: Theory and > Practice." This workshop will be presented on June 6-9, 1995 at > the CCC at University of Erlangen. The workshop will cover the full range > of methods available in the Gaussian 94 package with emphasis on new > methods and features which make Gaussian applicable to an ever widening > spectrum of questions. The workshop is structured to provide an introduction > to electronic structure theory as well as a hands-on review for researchers > active in the field. The workshop is open to researchers at all levels of > academic, government and industrial research. > > Please contact the Gaussian, Inc. offices for an application and further > details. > > Instructors: > > Dr. Michael J. Frisch Lorentzian, Inc. > Prof. H. Bernard Schlegel Wayne State University > Dr. Douglas J. Fox Gaussian, Inc. > Prof. Paul Schleyer CCC > > Tentative Agenda Topics: > > Introduction to Electronic Structure Theory > > MCSCF Methods and Applications > Geometry Optimization Techniques > Electron Correlation Methods > Density Functional Theory Methods > Excited States via CI Singlets > Thermochemistry via Model Chemistries > Interpretation of Results and Molecular Properties > Solvent Effects on Molecular Electronic Structure > Gaussian Utilities > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: FOX@cmchem.chem.cmu.edu > -- Original Sender From: Address: FOX@cmchem.chem.cmu.edu > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > > From cwm@proteus.co.uk Mon Mar 13 11:12:17 1995 Received: from eros.britain.eu.net for cwm@proteus.co.uk by www.ccl.net (8.6.10/930601.1506) id KAA16182; Mon, 13 Mar 1995 10:17:27 -0500 Received: from proteus.co.uk by eros.britain.eu.net with UUCP id ; Mon, 13 Mar 1995 15:16:37 +0000 From: Chris Murray Message-Id: <9503131435.ZM15860@Ivory.proteus.co.uk> Date: Mon, 13 Mar 1995 14:35:35 +0000 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: Summary:protein xray software Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear all, Here is the summary of responses I received from my question concerning the incorporation of more crystallographic information when using structure based drug design. I knew about the Biosym software which is nice in as far as it goes but there seems to be scope for more interesting integration. with thanks to all those who responded Chris My original question: The design of inhibitors to fit crystallographically determined protein structures often seems to assume that the structures are fixed. However there should be quite alot of information in the isotropic thermal parameters and the original diffraction data which could guide the designer about where to focus his/her designs in the first place. It ought to be possible also to represent this information graphically. Does anybody know of any software that does this? I will summarise if there is any interest. Chris Murray Proteus Molecular Design Ltd UK -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: cwm@proteus.co.uk -- Original Sender From: Address: cwm@proteus.co.uk CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV >From carlos%extreme.bio.cornell.edu%cornellc.cit.cornell.edu@uknet Mon Feb 27 18:18:20 1995 Received: from elliot by ivory.proteus.co.uk; Mon, 27 Feb 95 18:18:20 GMT Return-Path: Received: from CORNELLC.CIT.CORNELL.EDU by eros.britain.eu.net via EUnet with SMTP (PP) id ; Mon, 27 Feb 1995 15:35:52 +0000 Received: from extreme.bio.cornell.edu by CORNELLC.cit.cornell.edu (IBM VM SMTP V2R2) with TCP; Mon, 27 Feb 95 10:34:56 EST Received: by extreme.bio.cornell.edu (931110.SGI/921111.SGI) for @cornellc.cit.cornell.edu:cwm@proteus.co.uk id AA07826; Mon, 27 Feb 95 10:21:48 -0500 Date: Mon, 27 Feb 95 10:21:48 -0500 From: carlos@extreme.bio.cornell.edu (Carlos Faerman) Message-Id: <9502271521.AA07826@extreme.bio.cornell.edu> To: Chris Murray Subject: Re: CCL:protein xray software Status: OR Hello Chris, In answer to your question: 1) There is a program InsightII by Biosym that colors the protein according to the B-factors. It gives a rough idea of the areas which are poorly (greatly) defined. It is quite easy to use. Please let me know whether this is what you had asked Best regards Carlos Thanks Carlos H. Faerman carlos@extreme.bio.cornell.edu >From chemistry%dreamon.oxmol.co.uk@uknet Mon Feb 27 18:18:22 1995 Received: from elliot by ivory.proteus.co.uk; Mon, 27 Feb 95 18:18:22 GMT Return-Path: Received: from dreamon.oxmol.co.uk by eros.britain.eu.net via UKIP with SMTP (PP) id ; Mon, 27 Feb 1995 15:53:29 +0000 Received: from samson.oxmol.co.uk by dreamon.oxmol.co.uk via SMTP (920330.SGI/921111.SGI) for cwm@proteus.co.uk id AA16522; Mon, 27 Feb 95 15:55:15 GMT Date: Mon, 27 Feb 95 15:55:15 GMT Message-Id: <9502271555.AA16522@dreamon.oxmol.co.uk> X-Sender: chemistry@mailhost.oxmol.co.uk X-Mailer: Windows Eudora Version 2.0.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: Chris Murray From: chemistry@dreamon.oxmol.co.uk (Chemistry list) Subject: Re: CCL:protein xray software Status: OR > SH TRY ORTEP SURVIVING > >The design of inhibitors to fit crystallographically determined protein >structures often seems to assume that the structures are fixed. However there >should be quite alot of information in the isotropic thermal parameters and the >original diffraction data which could guide the designer about where to focus >his/her designs in the first place. It ought to be possible also to represent >this information graphically. Does anybody know of any software that does this? > >I will summarise if there is any interest. > >Chris Murray >Proteus Molecular Design Ltd >UK > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: cwm@proteus.co.uk >-- Original Sender From: Address: cwm@proteus.co.uk >CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator >MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 >Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search >http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > > >From haney%netcom.com@uknet Mon Feb 27 18:18:28 1995 Received: from elliot by ivory.proteus.co.uk; Mon, 27 Feb 95 18:18:28 GMT Return-Path: Received: from netcom10.netcom.com by ben.britain.eu.net via EUnet with SMTP (PP) id ; Mon, 27 Feb 1995 16:22:16 +0000 Received: by netcom10.netcom.com (8.6.9/Netcom) id IAA02039; Mon, 27 Feb 1995 08:20:28 -0800 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199502271620.IAA02039@netcom10.netcom.com> Subject: Re: CCL:protein xray software To: cwm (Chris Murray) Date: Mon, 27 Feb 1995 08:20:28 -0800 (PST) In-Reply-To: <9502271406.ZM13268@Ivory.proteus.co.uk> from "Chris Murray" at Feb 27, 95 02:06:54 pm X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 916 Status: OR Chris: I am also interested in this area and I would appreciate a summary of the info you receive. > The design of inhibitors to fit crystallographically determined protein > structures often seems to assume that the structures are fixed. However there > should be quite alot of information in the isotropic thermal parameters and the > original diffraction data which could guide the designer about where to focus > his/her designs in the first place. It ought to be possible also to represent > this information graphically. Does anybody know of any software that does this? -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** >From marvin%iris131.biosym.com@uknet Mon Feb 27 18:18:35 1995 Received: from elliot by ivory.proteus.co.uk; Mon, 27 Feb 95 18:18:35 GMT Return-Path: Received: from ns2.EU.net by eros.britain.eu.net via EUnet with SMTP (PP) id ; Mon, 27 Feb 1995 16:59:47 +0000 Received: from bioc1.biosym.com (bioc1.biosym.com [146.202.0.2]) by eunet.EU.net (8.6.10/8.6.10) with SMTP id RAA05944 for ; Mon, 27 Feb 1995 17:59:24 +0100 Received: from iris131.biosym.com by bioc1.biosym.com (5.64/0.0) id AA29858; Mon, 27 Feb 95 08:57:42 -0800 Received: by iris131.biosym.com (940816.SGI.8.6.9/930416.SGI) for cwm@proteus.co.UK id IAA15341; Mon, 27 Feb 1995 08:56:50 -0800 Date: Mon, 27 Feb 1995 08:56:50 -0800 From: marvin@biosym.com (Marvin Waldman) Message-Id: <199502271656.IAA15341@iris131.biosym.com> To: cwm Subject: RE:protein xray software Status: OR Hi Chris, Using InsightII, it is possible to color code the VDW or Connolly surface of a molecule based on the Temperature factor information stored in the PDB file. Here is an example of the appropriate commands for Crambin: m:Surface Molecule Create VDW CRN Dot 1 0 Medium -Context m:Color Molecule Surface CRN Specified Temperature_Factor TEMP_FACTOR_SPECTRM Regards, Marvin Waldman, Ph.D. Manager, Rational Drug Design Biosym Technologies, Inc. e-mail: marvin@biosym.com >From vijay%jellyfish.chem.wesleyan.edu@uknet Mon Feb 27 18:18:36 1995 Received: from elliot by ivory.proteus.co.uk; Mon, 27 Feb 95 18:18:36 GMT Return-Path: Received: from rose.chem.wesleyan.edu by eros.britain.eu.net via EUnet with SMTP (PP) id ; Mon, 27 Feb 1995 17:12:32 +0000 Received: from jellyfish.chem.wesleyan.edu by rose.chem.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA17211; Mon, 27 Feb 1995 11:24:33 -0500 Received: by jellyfish.chem.wesleyan.edu (NX5.67d/NX3.0S) id AA01418; Mon, 27 Feb 95 11:33:43 -0500 Date: Mon, 27 Feb 95 11:33:43 -0500 From: "S." Vijayakumar Message-Id: <9502271633.AA01418@jellyfish.chem.wesleyan.edu> Original-Received: by NeXT.Mailer (1.100) Pp-Warning: Illegal Received field on preceding line Original-Received: by NeXT Mailer (1.100) Pp-Warning: Illegal Received field on preceding line To: Chris Murray Subject: Re: CCL:protein xray software Status: OR Very true! They reflect the local flexibility of the different residues, which when taken into consideration can make a difference in the design of potential drugs. The anisotropic thermal factors where available could be even more helpful. We use a software called MD Toolchest here at Wesleyan, which is a collection of several different programs that interact with each other to analyze and produce graphical output. For a graphical presentation, we simply represent the thermal-factors as spheres (isotropic) or ellipsoids (anisotropic) of appropriate radii and project the molecule on to a plane based on the orientation specified by the user. If necessary one can select the residues comprising the active site alone. Hope that helps... Vijay ************************************************************* S. Vijayakumar, Ph. D., DCA Department of Chemistry, Wesleyan University, Middletown, CT 06459 Voice: (203) 685-2777 / 3213 Fax: (203) 685-2211 email: vijay@rose.chem.wesleyan.edu ************************************************************* >From shoba%atp.biochem.usyd.edu.au@uknet Tue Feb 28 09:19:40 1995 Received: from elliot by ivory.proteus.co.uk; Tue, 28 Feb 95 09:19:40 GMT Return-Path: Received: from atp.biochem.usyd.EDU.AU by eros.britain.eu.net via EUnet with SMTP (PP) id ; Mon, 27 Feb 1995 22:16:34 +0000 Received: from surya.biochem.usyd.EDU.AU (surya [129.78.130.73]) by atp.biochem.usyd.edu.au (8.6.9/8.6.9) with SMTP id JAA09598 for ; Tue, 28 Feb 1995 09:06:13 +1100 Message-Id: <199502272206.JAA09598@atp.biochem.usyd.edu.au> Sender: shoba From: Shoba Ranganathan To: Chris Murray Date: Tue, 28 Feb 1995 07:57:17 +0000 Subject: Re: CCL:protein xray software Reply-To: shoba@biochem.usyd.edu.au X-Mailer: Pegasus Mail/Windows (v1.22) Status: OR I would be interested in such software information - if you are not summarizing, could you kindly forward to me any replies that you get? Thank you. Shoba >From d.winkler%chem.csiro.au@uknet Tue Feb 28 09:19:43 1995 Received: from elliot by ivory.proteus.co.uk; Tue, 28 Feb 95 09:19:43 GMT Return-Path: Received: from auric.chem.CSIRO.AU by eros.britain.eu.net via EUnet with SMTP (PP) id ; Mon, 27 Feb 1995 22:50:44 +0000 Received: from chem.csiro.au (mac-40149.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA14378 (5.67b/IDA-1.5 for cwm@proteus.co.uk); Tue, 28 Feb 1995 09:44:01 +1100 Date: Tue, 28 Feb 95 09:49:47 EST From: "Dr." Dave Winkler Subject: Re: CCL:protein xray software To: Chris Murray X-Mailer: LeeMail 2.0.4 Message-Id: Status: OR >The design of inhibitors to fit crystallographically determined protein >structures often seems to assume that the structures are fixed. However there >should be quite alot of information in the isotropic thermal parameters and the >original diffraction data which could guide the designer about where to focus >his/her designs in the first place. It ought to be possible also to represent >this information graphically. Does anybody know of any software that does this? > This is a clever thought. >I will summarise if there is any interest. > Please do. (or send me a copy at any rate) Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 CSIRO: http://www.csiro.au Clayton, Australia. >From ng%tesla.mbi.ucla.edu@uknet Tue Feb 28 09:20:40 1995 Received: from elliot by ivory.proteus.co.uk; Tue, 28 Feb 95 09:20:40 GMT Return-Path: Received: from tesla.mbi.ucla.edu by eros.britain.eu.net via EUnet with SMTP (PP) id ; Tue, 28 Feb 1995 01:58:30 +0000 Received: by tesla.mbi.ucla.edu (5.57/Ultrix3.0-C) id AA02302; Mon, 27 Feb 95 17:58:55 -0800 Date: Mon, 27 Feb 95 17:58:55 -0800 From: ng@tesla.mbi.ucla.edu (Ng) Message-Id: <9502280158.AA02302@tesla.mbi.ucla.edu> To: cwm Subject: Re: CCL:protein xray software Status: OR I'd like to hear a summary of information you receive or if you uncover any interesting references. Thank you! Ho Leung Ng ng@tesla.mbi.ucla.edu >From martin%cmda.abbott.com@uknet Wed Mar 1 09:08:07 1995 Received: from elliot by ivory.proteus.co.uk; Wed, 1 Mar 95 09:08:07 GMT Return-Path: Received: from abtlabs.abbott.com by eros.britain.eu.net via EUnet with SMTP (PP) id ; Tue, 28 Feb 1995 20:41:30 +0000 Received: from randb.pprd.abbott.com (randb.abbott.com) by abtlabs.abbott.com with SMTP id AA27561 (5.65c/IDA-1.4.4 for ); Tue, 28 Feb 1995 14:38:27 -0600 Received: from DECNET-MAIL (MARTIN@CMDA) by RANDB.PPRD.Abbott.Com (PMDF V4.3-13 #5551) id <01HNL4FIKBO09I4CSA@RANDB.PPRD.Abbott.Com>; Tue, 28 Feb 1995 14:41:19 -0600 (CST) Date: Tue, 28 Feb 1995 14:41:19 -0600 (CST) From: MARTIN@cmda.abbott.com Subject: Re: CCL:protein xray software To: cwm Message-Id: <01HNL4FILXJ69I4CSA@RANDB.PPRD.Abbott.Com> X-Vms-To: RANDB::IN%"cwm@proteus.co.uk" X-Vms-Cc: MARTIN Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT Status: OR I certainly am interested in the response. Yvonne Martin Abbott Laboratories >From koehler%irbm.it@uknet Mon Mar 6 00:13:10 1995 Received: from elliot by ivory.proteus.co.uk; Mon, 6 Mar 95 00:13:10 GMT Return-Path: Received: from 192.167.2.64 by ben.britain.eu.net with SMTP (PP) id ; Sun, 5 Mar 1995 16:17:38 +0000 Date: Sun, 5 Mar 1995 17:13:52 +0100 (WET) From: "Konrad, IRBM Chemistry, +39-6-91093606" To: cwm Cc: KOEHLER@IRBM.IT Message-Id: <950305171352.7918@IRBM.IT> Subject: RE: CCL:protein xray software Status: OR Chris: It is possible to color code atoms according to crystallographic tempera- ture factors in Insight/Discover. As far as I can figure out, there is no corresponding functionality in Sybyl. I have just posted a message to the Sybyl newsgroup asking if anyone knew a way of doing this in Sybyl. Related to this issue, I just ran across a thought-provoking paper by Lumry[1] who argued that proteins should be classified according to internal structures defined by low temperature factors rather than the usual secondary structural elements. He described these low temperature factor networks of atoms as "knots". The extention of this idea to protein-ligand complexes is obvious. While I find Lumry's rabid anti-reductionist view point a little hard to take, I found the paper interesting nonetheless. [1] Lumry, R. The new paradigm for protein research. In "Protein - Solvent Interactions"; Gregory, R. B., Ed.; Marcel Dekker: New York, 1995; pp 1-141. I would appreciate receiving a summary of the responses to your posting. Likewise, if you have any references of the use of temperature factors in drug design, I would appreciate receiving them as well. 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 | ------------------------------------------------------------------ From ostertag@alf.biochem.mpg.de Mon Mar 13 12:12:21 1995 Received: from nmrvex.biochem.mpg.de for ostertag@alf.biochem.mpg.de by www.ccl.net (8.6.10/930601.1506) id LAA17610; Mon, 13 Mar 1995 11:27:28 -0500 From: Received: from assel.biochem.mpg.de by nmrvex.biochem.mpg.de (5.64/1.35) id AA06882; Mon, 13 Mar 95 17:27:05 +0100 Received: from localhost by alf.biochem.mpg.de; (5.65/1.1.8.2/04Oct94-0534PM) id AA16650; Mon, 13 Mar 1995 17:27:03 +0100 Message-Id: <9503131627.AA16650@alf.biochem.mpg.de> To: chemistry@ccl.net Subject: calculating transition dipol moments? Date: Mon, 13 Mar 95 17:27:02 +0100 X-Mts: smtp Dear Netters, I want to calculate transition dipol moments of fluoreszent dyes (30-50 atoms) with MOPAC (AM1). Can someone tell me, what I have to do? (As you can see, I'm completely new to this matter). _ALL_ answers are welcome! Georg Ostertag ostertag@alf.biochem.mpg.de From gavin@vangogh.chem.uab.edu Mon Mar 13 12:19:12 1995 Received: from vangogh.chem.uab.edu for gavin@vangogh.chem.uab.edu by www.ccl.net (8.6.10/930601.1506) id LAA17297; Mon, 13 Mar 1995 11:18:12 -0500 From: Received: by vangogh.chem.uab.edu (AIX 3.2/UCB 5.64/4.03) id AA16096; Mon, 13 Mar 1995 10:12:04 -0600 Date: Mon, 13 Mar 1995 10:12:04 -0600 Message-Id: <9503131612.AA16096@vangogh.chem.uab.edu> To: CHEMISTRY@ccl.net Subject: INSTABILITY and SYMMETRY-BREAKING Dear Netters, I used G92/DFT to the ONOONa molecule. In HF/6-311+G* calculations, the O=N vibration frequency is 1718 cm(-1) and the MP2/6-311+G* frequency is 2408 cm(-1). There is 700 cm-1 change from HF to MP2. The IR intensity of MP2 calculations is very large and out of the Gaussian's format. The vibration frequency of this molecule is very sensitive to the basis set! I guess these unusual results are caused by the instability and symmetry-breaking of wavefunctions. The MP2/HF calculations do not agree with EXP. results. The Becke3LYP results are well agreenment with the IR spectra. Anyone has ideas about this topics? Thanks ! Gavin Tsai From THOMPSON@JAGUAR.CSC.WSU.EDU Mon Mar 13 15:14:54 1995 Received: from JAGUAR.CSC.WSU.EDU for THOMPSON@JAGUAR.CSC.WSU.EDU by www.ccl.net (8.6.10/930601.1506) id PAA22974; Mon, 13 Mar 1995 15:02:20 -0500 Date: Mon, 13 Mar 1995 11:32:22 -0800 (PST) From: "Steve Thompson: VADMS genetics" To: dunker@jaguar.csc.wsu.edu, thompson@jaguar.csc.wsu.edu, prcadams@jaguar.csc.wsu.edu, Sogin@evol1.MBL.EDU, gary@phylo.life.uiuc.edu, Davison@UH.EDU, Joe@Genetics.Washington.EDU, gilbertd@bio.indiana.edu, chod21633@ggr.co.uk X-Vmsmail-To: @MAILDIS:EDUCATION.DIS Message-Id: <950313113222.204066c1@JAGUAR.CSC.WSU.EDU> Subject: Pacific Symposium on Biocomputing: Education track interest Dear Colleague - You might or might not be aware of the Pacific Symposium Biocomputing conference to be held January 3 to 6, 1996 in Hawaii (see announcement after this letter). Please notice that an effort is being made to organize a session or track on educational issues, but to do this a proposal will have to be submitted by March 18. We are interestesed in organizing this track. You could help us greatly in the development of a proposal by providing us with the following information: Name Address e-mail address courses or workshops you are teaching in the broadly defined field of "biocomputing" and the year such courses or workshops began. A brief statement of your willingness to participate in the 1996 meeting as one: who would submit a paper by early June describing course, workshop or curriculum issues and who would subsequently attend the meeting to present the paper if accepted; who would plan to attend the meeting, participate in panel discussions, software demonstrations, and workshops on educational issues, but who would not submit a paper; who might or might not attend the meeting, but who would be willing to review papers. Finally, could you please provide names and addresses of others who might be interested in participatingn in the educational session. Sincerely - A. Keith Dunker Susan J. Johns Department of Biochemistry Steve Thompson VADMS Center Department of BioChemistry & BioPhysics Visualization, Analysis & Design in the Molecular Sciences Washington State University, Pullman, WA 99164-1224, USA -------------------- attached symposium announcement ---------------------- Call For Track Proposals Pacific Symposium on Biocomputing Hawaii - January, 1996 This is an invitation to submit proposals for tracks in the first Pacific Symposium on Biocompting (PSB), to be held January 3-6, 1996 in Hawaii. PSB will bring together top researchers from the US, the Asian Pacific nations and around the world to exchange research results and address open issues in all aspects of computational biology. Replacing and extending the last three years of Biotechnology Computing Tracks at the Hawaiian International Conference on System Sciences, PSB will provide a forum for the presentation of work in databases, algorithms, interfaces, visualization, modelling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. In addition, PSB intends to attract a more balanced combination of computer scientists and biologists by reducing some of the barriers to the attendence of biologists reported by HICSS participants. The PSB will be organized into specific tracks, to provide focus for the very broad area of biological computing. Proposals for such tracks are hereby solicited. A track proposal should identify a coherent topic that can be addressed by 3 to 12 papers. For example, a track might bring together papers on alternative approaches to a particular biological question or it might examine the applications of a particular technology in a variety of biological areas. Possible tracks for PSB include, but are not limited to: * Education and curriculum for computational biology * Advances in molecular visualization * Parallel computation for molecular biology * Emerging technology for genome databases * New methods for phylogenetic inference A general track, two invited addresses, live computer demonstrations and a poster session will round out the schedule. Responsibilities of a track chair: As a proposer of an accepted track, you will become the track chair. The chair's primary responsibility is to solicit high quality papers for the track and oversee their review. You are to solicit manuscripts, have them refereed, collaborate with the conference chairs in determining which manuscripts are to be accepted and structure the sessions in your track. Procedure for submitting proposals: Track proposals can be as short as a single page and should in no case be more than 6 pages. The proposal should: * Define a specific technical area to be covered. * Justify why the proposed area is appropriate for PSB. Discuss why the topic is timely and important, and how the topic has been addressed in other conferences or recent publications. * Argue that there is likely to be sufficient high quality, unpublished material to fill the track, e.g., a list of researchers you intend to solicit for papers. * Provide a short autobiographical sketch and an explicit statement that your organization endorses your involvement. We highly encourage the submission of proposals by e-mail. If sent by surface mail, send five copies. The deadlines are: March 18, 1995 Proposals Due April 5, 1995 Notification Regarding the Proposals Each proposal will be evaluated by the organizing committee: Lloyd Allison, Australia Juergen Brickmann, Germany Janice Glasgow, Canada Lawrence Hunter, USA (co-char) Teri Klein, USA (co-chair) Toshihisa Takagi, Japan We look forward to your submissions. Send proposals to: Dr. Teri Klein Computer Graphics Laboratory University of California, San Francisco San Francisco, CA 94143-0446 phone: (415) 476-0663 fax: (415) 502-1755 email: klein@cgl.ucsf.edu From ryan@phu198.mms.sb.com Mon Mar 13 16:12:05 1995 Received: from phu198.mms.sb.com for ryan@phu198.mms.sb.com by www.ccl.net (8.6.10/930601.1506) id PAA23211; Mon, 13 Mar 1995 15:12:06 -0500 Received: by phu198.mms.sb.com (940816.SGI.8.6.9/931108.SGI.AUTO.ANONFTP) for CHEMISTRY@ccl.net id OAA02884; Mon, 13 Mar 1995 14:59:32 -0500 Date: Mon, 13 Mar 1995 14:59:32 -0500 From: ryan@phu198.mms.sb.com (Dominic Ryan) Message-Id: <199503131959.OAA02884@phu198.mms.sb.com> To: CHEMISTRY@ccl.net Subject: Color by temp. factor Reply-To: ryan%phu198.mms@sb.com I like MidasPlus from UCSF. It will color by temperature factor or a variety of other criteria. It is a display-only package, i.e. no min or md etc. but it is certainly a lot less expensive that InsightII and very well suited for protein visualization. __ M. Dominic Ryan (610)-270-6529 SmithKline Beecham Pharmaceuticals Internet: ryan%phu198.mms@sb.com King of Prussia, PA From rsjuds@california.sandia.gov Mon Mar 13 16:23:58 1995 Received: from california.sandia.gov for rsjuds@california.sandia.gov by www.ccl.net (8.6.10/930601.1506) id PAA24384; Mon, 13 Mar 1995 15:49:15 -0500 Received: by california.sandia.gov (8.6.10/1.15) id MAA12782; Mon, 13 Mar 1995 12:49:12 -0800 From: rsjuds@california.sandia.gov (judson richard s) Message-Id: <199503132049.MAA12782@california.sandia.gov> Subject: Rigid body minimization, summary To: chemistry@ccl.net Date: Mon, 13 Mar 1995 12:49:11 -0800 (PST) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 9151 Sometime back, I posted the following query, and got a number of responses, which are included below. Thanks all! ------------------------------------------------------------- We are starting to look at rigid body gradient optimization of ligands inside protein cavities. I am looking for information on what the best methods and implementations are. For instance have people used truncated Newton methods vs. CG methods? Are implementations in one commercial package superior to those in another? Does converting to all internal coordinates work much better than using cartesians plus Lagrange multiplier constraints? Any information is useful. I will summarize if there is interest. ----------------------------------------------- | Richard Judson | | Center for Computational Engineering, MS 9214 | | Sandia National Laboratories | | Livermore, CA 94551-0969 | | (510)294-1438 | | (510)294-2234 (FAX) | | email: rsjuds@ca.sandia.gov | | | ----------------------------------------------- Dear Richard, If you are talking about rigid ligand and rigid enzyme, you will have only 6 variables: 3 translation and 3 rotation. In that case, quasy-newton methods (e.g. BFGS) are superior CG or truncated Newton. I used 2 approaches: (i) rigid coordinates, R, Theta, Phi, A, B, C - where (R, Theta, Phi) determine position of the center mass of ligand relative to enzyme's center mass and A, B and C are rotational angles. (ii) internal coordinates. In my experience, internal coordinates of ligand are better for optimization. Using this coordinates, it is also easy to add flexibility to the ligand. Internal coordinates are also help, when doing simulated annealing (or any random based search), because it easy to add constrains to the length of ligand - enzyme bond. Otherwise, ligand, sometimes, has a tendency to fly away from the active site. Andrey I forgot to add: I would certainly be interested in what other people have to say on this subject. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- those in another? Does converting to all internal coordinates work much better than using cartesians plus Lagrange multiplier constraints? I would expect that. First of all, I must say that I have no experience at all with minimization, but I do have with dynamics. However, the two problems are sufficiently similar. Using Lagrange multipliers in a straightforward way will not satisfy the constraints well over many time steps, due to the accumulation of numerical errors. The common solution for dynamics is an algorithm calles SHAKE, which uses an iterative method to satisfy the constraints exactly after each step. This works well for some types of constraints, but badly or not at all for others, as the convergence of the iterative algorithm can become very bad. Some problems - like keeping more than three particles in a plane - cannot be handled at all in this way. Another problem with Lagrange multipliers is that you have to be careful in the choice of constraints. You could define a rigid body by keeping the distances between all atom pairs fixed, but for more than three particles this will lead to redundant constraints. You must then select exactly the right number of constraints to get the right number of degrees of freedom, and of course not all possible choices will be equally good in terms of convergence. A description of how to do dynamics in internal coordinates and avoiding all these problems can be found in G.R. Kneller & K. Hinsen Phys. Rev. E 50, 1559 (1994) Another paper on an implementation and application of this method is in preparation. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- [ On Mon, 23 Jan 1995 17:44:35 -0800 (PST) ] [ rsjuds@california.sandia.gov (judson richard s) wrote: ] [ ... ] Judson> Any information is useful. I will summarize if there is interest. There is interest, I would appreciate if you could summarize/post your information. -- Thank you, -- Marcel ______________________________________________________________________ Marcel TURCOTTE -- Universite de Montreal http://www.IRO.UMontreal.CA/people/turcotte ______________________________________________________________________ Dear Dr Judson I would appreciate a copy of any summary you put together for the above question. Many thanks David E. Clark | Proteus Molecular Design Ltd., | Tel: 01625-500555 Lyme Green Business Park, | Fax: 01625-500666 Macclesfield, Cheshire, | Email: D.E.Clark@proteus.co.uk SK11 0JL, UK | Dear Richard, could you keep me informed of the responses you get. I'm very interested in this topic since I'm doing similar things, optimising molecules (ions) in crystaline cavities. Up to now I've used euler angles + gradients to do the optimisation but sometimes get into trouble because of non-continuous changes in the angles. many thanks, kris van alsenoy alsenoy@uia.ua.ac.be ------------------------------------------------------------------- Please summarize! Thanks. Eric Walters * D. Eric Walters, Ph.D., Associate Professor, Biological Chemistry * Finch University of Health Sciences/The Chicago Medical School * 3333 Green Bay Road, North Chicago, IL 60064 * ph 708-578-3000, x-498;fax 708-578-3240; email: walterse@mis.fuhscms.edu * "A man would do nothing if he waited until he could do it so well that * no one would find fault with what he had done." --Cardinal Newman Dear Dr. Judson I would like to ask you to send me replies you have got ( or will get). I am also interested in rigid body dynamics. Best wishes Grzegorz Bakalarski grad. stud. in Dep. of Biophys. Warsaw University Poland I'm interested...please summarize. I don't remember if you've ever used it, but the software marketed by a company I used to work for, BioDesign (now part of MSI), had a function like this, but I don't know the details of how it worked. The products were called Biograf and Polygraf. I think the rigid body minimization stuff was designed by Bill Goddard and Marv Goodgame at Caltech. I can get in touch with Marv to ask him more details, if you don't get them from elsewhere. Wally ======================================================================== Walter E. Reiher III, Ph.D. WallyR@netcom.com Consultant in Computational Chemistry P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 Hi, Richard I wrote a rigid-body minimizer for exactly this application back in 1980-81, while I was at UCSF. It was described in my thesis, but never published (I didn't think anybody would be interested). The only publication that refers to it is Kuntz' group at UCSF: Meng, E. C., Gschwend, D. A., Blaney, J. M., Kuntz, I. D. "Orientational Sampling and Rigid-Body Minimization in Molecular Docking", Proteins 1993, 17, 266-278. I'll send you a copy of the paper, and even the program, if you're interested. I've never seen anything else that compares to it. My group at DuPont used it through most of the 80's, so did Scott Dixon's group at Smith Kline. I don't use it much anymore - I do all our docking work with distance geometry now. I wrote it in Fortran-77. This was my first major program, so the code isn't really pretty, but it works well. It works in Euler space using numerical derivatives with a DFP minimizer. Its very fast; just takes a few seconds to do a local optimization from a manually docked ligand position. I never worked on any approaches for global optimization with this - I just wanted it to clean up manual dockings before investing in full-scale, all degrees of freedom, optimizations. Jeff Dear Dr. Judson, Some time ago you posted a question on the compchem newsgroup regarding methods to perform rigid body optimization of ligands in protein cavities. I would very much appreciate a summary of responses. Thank you. -- ----------------------------- Paul Rejto, Ph.D. Research Scientist Agouron Pharmaceuticals, Inc. 3565 General Atomics Court San Diego, CA 92121 (619) 622-3149 rejto@agouron.com From jkl@ccl.net Mon Mar 13 16:24:58 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.10/930601.1506) id QAA24768; Mon, 13 Mar 1995 16:06:54 -0500 Date: Mon, 13 Mar 1995 16:06:54 -0500 From: Jan Labanowski Message-Id: <199503132106.QAA24768@www.ccl.net> To: chemistry@ccl.net Subject: ACES II workshop/quantum chemstry Cc: jkl@ccl.net, yanke@qtp.ufl.edu Dear Colleague: We are pleased to announce an ACES II Workshop, conducted by authors of the program, that will be held from May 17-20, 1995, at the University of Florida in Gainesville, Florida. Through a cooperative agreement with Silicon Graphics, Inc., the workshop will be conducted on SGI Indigos. Further details are on the attached announcement. To take advantage of inexpensive plane fares that include a Saturday night stay, the course is scheduled for Wednesday through Saturday, May 17-20, with arrival on Tuesday night, May 16, and recommended departure on Sunday, May 21, 1995. Overview lectures coupled with computer lab sessions are scheduled for Wednesday, Thursday, and Friday, with all day Saturday, May 20, scheduled for additional work on applications. We also devote time to hear about your research problems and try to assist you in using ACES II to help solve them. Social events include a welcoming reception Tuesday evening and dinners Wednesday and Friday, held at the best restaurants in the area. Tuition, which includes lodging, two special dinners, daily continental breakfasts, and detailed lecture notes, is at an inclusive $750 per person. Enrollment will be limited to 20 participants, housed in single rooms at the Reitz Union on the University of Florida campus. Although the course is intense, companions are invited to accompany a participant by payment of an additional $100 to cover the social affairs. If you are interested in registering for our workshop, please contact Mrs. Yanke in my office at (904) 392-1597 or by e-mail (yanke@qtp.ufl.edu). Registration plus a check or purchase order payable to the University of Florida Research Foundation will be required by May 1, 1995, and should be sent directly to me at the Quantum Theory Project, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435. We hope that you or some of your colleagues will find our course to be of interest. If we can provide any further information, please contact us. Sincerely, Rodney J. Bartlett Graduate Research Professor of Chemistry and Physics RJB:kjy Attachment * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ACES II WORKSHOP May 17-20, 1995 - University of Florida - Gainesville, Florida Advanced Concepts in Electronic Structure II (ACES II) is a very fast, easily used program directed at high-level, correlated, ab initio studies of molecules. It offers the most modern methods based upon coupled-cluster (CC) theory and its finite-order, many-body perturbation theory (MBPT=MP) approximations; all augmented by analytical gradients; as well as density functional theory (DFT). The program offers many unique, recently developed methods that open new vistas for application. All correlated calculations exploit symmetry through D2h, making the program unusually fast for applications to symmetric molecules. With the cooperation of Silicon Graphics, Inc., this "hands-on" workshop will demonstrate how to perform correlated ACES II applications for the following topics: Energies, Molecular Structures, and Vibrational Spectra Electronic Excited States and UV-vis Spectra NMR Shielding Constants NMR Spin-Spin Coupling Constants Photoelectron Spectra Molecular Properties, like Moments, Spin Densities, Field Gradients, etc. Polarizabilities and Hyperpolarizabilities And many other topics... All the above apply the newest techniques based on coupled-cluster (CC) theory, including triple excitations, with restricted, restricted open shell, unrestricted, and quasi-restricted (RHF, ROHF, UHF, QRHF) reference functions with analytical gradients; for excited states, the new equation-of-motion coupled-cluster (EOM-CC) theory and the two-determinant (TD-CC) theory; for ionization and electron attachment processes (EOM-IP CC and EOM-EA CC); for first-order properties, the CC/MBPT "relaxed density" approach; and for second-order properties, EOM-CC. The methods are described in overview lectures followed by supervised applications on SGI Indigos designed to illustrate the approach. Time is also provided to enable you to investigate your own applications with expert assistance. We also address topics like computer resource management. Attendance is limited to 20 people on a first-come basis. For further information: Rodney J. Bartlett Quantum Theory Project University of Florida P. O. Box 118435 Gainesville, FL 32611-8435 (904) 392-1597 or aces2@qtp.ufl.edu From rao@ddix4.monsanto.com Mon Mar 13 17:14:36 1995 Received: from tin for rao@ddix4.monsanto.com by www.ccl.net (8.6.10/930601.1506) id QAA26102; Mon, 13 Mar 1995 16:55:56 -0500 Received: from ddix4.monsanto.com by tin (5.65/Monsanto1.7) id AA19888; Mon, 13 Mar 1995 15:55:21 -0600 Received: by ddix4.monsanto.com id AA20799; 931110.SGI/CRI-%I%; Mon, 13 Mar 95 15:55:20 -0600 From: "Shashi Rao" Message-Id: <9503131555.ZM20797@ddix4.monsanto.com> Date: Mon, 13 Mar 1995 15:55:19 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: postponement of the CCCC seminar to 4/13/95 Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 March 13, 1995 Since quite a few Chicago area computational chemists will be attending the ACS meeting at Anaheim on 4/6/95, the seminar by Dr. Joe Golab scheduled for that day has been postponed to 4/13/95. Everything else about the seminar remains the same (i.e. place, directions, title of the talk, availability of pizza). The seminar specifics are included once again for convenience. Upon reaching the Amoco Research Center, please identify yourself as coming to the "CCCC meeting in Building 602" to the security officials. Please contact Dr. Joe Golab ((708) 961-7878) for further details. Shashi Rao ================================================================ The Chicago Computational Chemistry Club Presents Dr. J. T. Golab Amoco Research Center "What is Chemistry Modeling?: An Industrial Perspective" Thursday, the 13th April, 1995 at 7:30 p.m. (Pizza at 6:30 p.m.). Venue : Amoco Research Center, Building 602, Room 1218, Naperville. Abstract: ======== Modeling by computational methods can be a general purpose, less expensive alternative to the traditional experimental methods of problem solving. Advances in software and hardware technologies have made the use of computational chemistry techniques practical for industrial applications. As a result, chemistry modeling is slowly becoming more mainstream in industrial R&D, although it is still considered a relatively unproven information source. In this talk, we will discuss the foundations of chemistry modeling in regards the kinds of industrial problems it can help solve. We will also discuss several current examples; in particular a recent computational survey of methane to methanol catalysis based on compounds containing third row transition metals. Finally, the promise of chemistry modeling as a modern business tool will be addressed. Directions : =========== To get to Amoco Research Center: From West or East bound I-88 take the Naperville Road exit and turn left (North) onto Naperville Road. The first street light is Warrenville Road; turn left (West) onto Warrenville. Proceed approximately 1.5 miles to Herrick Road; turn left (South) into the Amoco Research Center. From nauss@ucmod2.che.uc.EDU Mon Mar 13 21:12:11 1995 Received: from ROCK.SAN.UC.EDU for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.10/930601.1506) id UAA29270; Mon, 13 Mar 1995 20:12:38 -0500 Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.3-10 #7238) id <01HO391VBYAO8WW2II@UCBEH.SAN.UC.EDU>; Mon, 13 Mar 1995 14:07:40 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:CHEMISTRY@ccl.net id AA14030; Mon, 13 Mar 95 14:10:50 -0500 Date: Mon, 13 Mar 1995 14:10:50 -0500 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Spelling question To: CHEMISTRY@ccl.net Reply-to: nauss@ucmod2.che.uc.EDU Message-id: <9503131910.AA14030@ucmod2.che.uc.edu> Content-transfer-encoding: 7BIT Sorry about the rather mundane question but... We have a minor controversy here. What is the correct spelling for van der Waals parameters or forces? Is it: a. van der Waal's parameters (lower case v and apostrophy) b. Van der Waal's parameters (upper case v and apostrophy) c. van der Waals parameters (lower case v and no apostrophy) d. Van der Waals parameters (upper case v and no apostrophy) e. some other permutation? Any comments from journal editors out there? Thanks in advance. I will report a concensus opinion (if any) for the net. 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://ucmodl.che.uc.edu/~nauss/homepage.html * **************************************************************************** From 5GK9SUNJ@VMS.CSD.MU.EDU Mon Mar 13 23:13:26 1995 Received: from VMSA.CSD.MU.EDU for 5GK9SUNJ@VMS.CSD.MU.EDU by www.ccl.net (8.6.10/930601.1506) id XAA01039; Mon, 13 Mar 1995 23:09:20 -0500 Received: from VMS.CSD.MU.EDU by VMS.CSD.MU.EDU (PMDF V4.3-10 #8872) id <01HO3PS1A8U891ZA9J@VMS.CSD.MU.EDU>; Mon, 13 Mar 1995 22:09:18 -0600 (CST) Date: Mon, 13 Mar 1995 22:09:18 -0600 (CST) From: "JIANGUO SUN, CHEMISTRY DEPT., MARQUETTE U." <5GK9SUNJ@VMS.CSD.MU.EDU> Subject: Where are chemistry WWW webs? To: chemistry@ccl.net Message-id: <01HO3PS1AIHE91ZA9J@VMS.CSD.MU.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: 5GK9SUNJ MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters: Could anyone tell me where I can find some WWW webs about chemisty resources? I need some samples (any chemistry) so that I can build ours. Thanks in advance. J. Sun