From epw@ppco.com Mon Dec 20 08:57:42 1993 Received: from newton.ncsa.uiuc.edu for epw@ppco.com by www.ccl.net (8.6.4/930601.1506) id IAA09926; Mon, 20 Dec 1993 08:09:42 -0500 Received: from ppco.com by newton.ncsa.uiuc.edu with SMTP id AA24484 (5.65a/IDA-1.4.2 for chemistry@ccl.net); Mon, 20 Dec 93 07:09:38 -0600 Received: from [0.0.0.0] (epwpc.ppco.com) by ppco.com (4.1/SMI-4.1) id AA14674; Mon, 20 Dec 93 07:10:07 CST From: "Eric P. Wallis" Date: Mon, 20 Dec 93 07:09:42 CST Message-Id: <1445.epw@charon_POPMail/PC_3.2.3_Beta_2> Reply-To: X-Popmail-Charset: English To: chemistry@ccl.net Subject: Re: De Novo Drug design Andy Holder makes some very valid points about the over selling of computational chemistry (CC). The idea that CC can be used, without experimentation, to bring a product to production scale is ludicrous. CC is a method that can help accelerate the research time and decrease the scale-up time as well as providing information when experimentation is not availible or accessible. Over selling of CC as an independent means of developing new products will only drive this method out of industry. This is my $.02 on this subject. On Fri, 17 Dec 1993 17:03:10 -0600 (CS, Andy Holder wrote: >Hi Netters! > >I read with interest an earlier question requesting info about some >drugthat was designed from computational modelling. About two years >ago, I asked for "semiempirical success" stories on thsi net and got a >rather low response. Given my interest on a variety of fronts, I have >been thinking about this for sometime. Please excuse the soapbox, but I >would like to share some of my thoughts and those of others I have >collected over the past few years on this issue: > > Drug companies and other chemical manufacturers are not going to >tell you about this even if they have an example. This type of stuff is >usually proprietary. > > Is this really the correct question to ask about computational >chemistry (CC from here on)? What is it that we expect CC to accomplish >for us? Is it going to replace experimental investigations? > > I look at CC in a company's product discovery cycle as a contributor to >the process, not an end in itself. CC will NOT replace experimental >information or procedures. We should not tell management (whether >scientific or "lay") that it will. We should not try to sell it on >this basis. The CC out there now is based on a set of models that are >imperfect. These imperfections are present from molecular mechanics >through semiempirical to ab initio methods. I admit they are getting >better and more reliable (I work quite hard along these lines myself in >the area of semiempirical methods) but they will never replace direct >observations. > > How then should CC be viewed? I think an excellent analogy is the way >we think about the analytical chemistry (AC) division of any large res- >earch operation. AC supports efforts in all phases of the research >process. However, the mass spec guy is never asked "What specific drug >product is that there $500,000 GC/MS dohicky responsible for?" Everyone >recognizes that the mass spec is part of the effort, and things would be >crippled without it. > > This is how CC should be integrated into the research/discovery process. >There are several models on how to include CC in a company's effort. In >one, the CC guys are a consulting group that works with people that >bring them specific problems. In another, each effort has one or more >CC guys IN the group. Both are valid and both seem to be producing >results. CC is good are predicting trends and in focusing experimental >investigations, which are fairly expensive these days. CC should be >part of every research problem in a modern setting. PART, I said, not >WHOLE. > > Alot of the recent "backlash" against CC is due to overselling. If >we CC folk expect to survive, we don't need to oversell the results that >we can provide, but honestly point out what CC should be doing. > > To finish, I'll tell a little story. When I was interviewing for a >job on leaving the Dewar group about 6 years ago, I visited the research >labs of a large midwestern polymer manufacturer. I was shown a lab with >4 PhD polymer chemists in it. Each was required to make 1 new polymer >blend per week. These blends then went to physical testing for >evaluation as new products. The company expected to get one new >CANDIDATE for a new product each year out of that lab. Seems a bit >cost prohibitive doesn't it? They asked me how CC could help them. >Back then, the answer was much less positive than it is now, but even >then, CC could have helped them focus their efforts more directly and >greatly enhanced the "hit rate." IMHO, that's what we do best. > > Hope this wasn't too preachy..... > > > > Andy Holder > >ps I welcome comments from others, especially our industrial brethren. > >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > DR. ANDREW HOLDER > Assistant Professor of Computational/Organic Chemistry > >Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 >University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu >Spencer Chemistry, Room 315 || Phone Number: (816) 235-2293 >Kansas City, Missouri 64110 || FAX Number: (816) 235-1717 >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > >---Administrivia: This message is automatically appended by the mail exploder: >CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator >MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net (port 70 or 73) >Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search ***************************************************** Dr. Eric P. Wallis Computational Chemistry Phillips Petroleum Co. (918) 661-7956 Voice 331A PL (918) 662-1097 FAX Bartlesville, OK 74004 epw@ppco.com e-mail ***************************************************** From ivar@chem.ut.ee Mon Dec 20 11:58:59 1993 Received: from piko.chem.ut.ee for ivar@chem.ut.ee by www.ccl.net (8.6.4/930601.1506) id LAA12425; Mon, 20 Dec 1993 11:38:51 -0500 Received: by piko.chem.ut.ee (Smail3.1.27.1 #2) id m0pBncx-0001lsC; Mon, 20 Dec 93 18:38 EET Message-Id: Subject: Mopac 6.0 for DOS To: chemistry@ccl.net Date: Mon, 20 Dec 1993 18:38:34 +0200 (EET) From: Ivar Koppel X-Mailer: ELM [version 2.4 PL0] Content-Type: text Content-Length: 746 Some weeks ago somebody was interested in MOPAC running under DOS. Now I can say that we have ported MOPAC 6.0 under MSDOS. It can handle currently 38+38 atoms and is basicly the same program as for VMS or IBM (currently only time and date functions are missing i.e date is Today and time is 00 sec). In my 33 Mhz 486 with 4 M RAM it runs as fast as under Linux, compleately in RAM. (No swapping required). It was compiled using DJ Delories Gnu CC port to MSDOS (DJGPP) and f2c compiler. The size of .EXE file is ca 1.3 Mb, the only program you need to run MOPAC is a small program called go32.exe from DJGPP GCC package (free). If you are interested, send E-mail to ivar@chem.ut.ee or peeter@chem.ut.ee. Best regards, Ivar. From mwitten@chpc.utexas.edu Mon Dec 20 12:57:44 1993 Received: from twilight.chpc.utexas.edu for mwitten@chpc.utexas.edu by www.ccl.net (8.6.4/930601.1506) id MAA13141; Mon, 20 Dec 1993 12:23:40 -0500 From: Received: by twilight.chpc.utexas.edu (4.1/SMI-4.1) id AA13078; Mon, 20 Dec 93 11:23:23 CST Date: Mon, 20 Dec 93 11:23:23 CST Message-Id: <9312201723.AA13078@twilight.chpc.utexas.edu> To: CHEMISTRY@ccl.net Subject: VIRTUAL REALITY IN MEDICINE From 70530.1227@CompuServe.COM Mon Dec 20 11:18:23 1993 Return-Path: <70530.1227@CompuServe.COM> Received: from dub-img-2.compuserve.com by hermes.chpc.utexas.edu (5.64/SMI-3.2) id AA23840; Mon, 20 Dec 93 11:18:21 -0600 Received: from localhost by dub-img-2.compuserve.com (8.6.4/5.930129sam) id MAA14210; Mon, 20 Dec 1993 12:18:20 -0500 Date: 20 Dec 93 12:12:07 EST From: Karen Morgan <70530.1227@CompuServe.COM> To: "Matthew Witten, Ph.D." Subject: MMVRII Message-Id: <931220171206_70530.1227_CHV41-1@CompuServe.COM> Status: RO I hope the plans for your World Congress are going well. We'd like to do an announcement to be distributed via your electronic mailer system, as you offered previously. Please publish the following abbreviated program: Medicine Meets Virtual Reality II: INTERACTIVE TECHNOLOGY AND HEALTHCARE: VISIONARY APPLICATIONS FOR SIMULATION, VISUALIZATION, ROBOTICS January 27-30, 1994, San Diego Marriott Hotel & Marina Sponsored by UCSD, 23 hours Category 1 CME credit, $390 until December 31, $450 after, call 619/751-8841, fax 751-8842, or E-mail 70530,1227@compuserve.com for information THURSDAY, January 27, three workshops offered simultaneously: I. BIOLOGICAL INFORMATICS, Hans B. Sieburg, Ph.D., Chair, Participants: Sheldon Ball, Floyd Bloom, Michael Huerta, Ralph Martinez, Jack Park, Stella Veretnik, W. Ziarko II. MASSIVELY PARALLEL PROCESSING COMPUTERS FOR MEDICAL TECHNOLOGY DEVELOPMENT Makoto Nonaka, M.D., Ph.D., Chair, Participants: Adrian King, Patrick Chang, Michael Gribskov, Russ Altman, Tom Brotherton III.INTERACTIVE TECHNOLOGIES IN HEALTHCARE: THE "BIG PICTURE" Dave Warner, Chair FRIDAY, January 28 TECHNOLOGY ASSESSMENT: Who Will Pay and Why? Diane S. Millman, J.D., Paul Radensky, M.D., J.D., John E. Abele, Steven T. Charles, M.D., Mark Wiederhold, M.D., Ph.D., Faina Shtern, M.D., Melvyn Greberman, M.D., MPH DATA FUSION: More Than the Sum of the Parts. Don Stredney, Hans B. Sieburg, Ph.D., Mark Wiederhold, M.D., Ph.D. APPLICATIONS: New Visions for New Technologies. Col. Richard M. Satava, M.D., Joseph M. Rosen, M.D., Harvey Eisenberg, M.D., Michael D. Doyle, Ph.D., Walter J. Greenleaf, Ph.D., John P. Brennan, M.D., Kenneth Kaplan, Beth A. Marcus, Ph.D., Suzanne Weghorst, Christopher C. Gallen, M.D., Ph.D. SURGERY: Images of the New Paradigm. Glenn M. Preminger, M.D., John Flynn, Adrie C.M. Dumay, Ph.D., David Hon, Jonathan R. Merril, M.D., Zoltan Szabo, Ph.D., Michael Truppe, M.D., Patrick J. Kelly, M.D., Robert B. Lufkin, M.D., Leon Kaufman, Ph.D., Karun Shimoga, Ph.D., William E. Lorensen, Volker Urban, M.D., P. Mayer, N. M. Huewel, M.D. SATURDAY, January 29 EDUCATION AND TRAINING: The Best and Highest Use. J.K. Udupa, Ph.D., Richard A. Robb, Ph.D., Jonathan Prince, D.D.S., Helene M. Hoffman, Ph.D., Michael J. Ackerman, Ph.D. INTERFACE: Speaking the Same Language. Nathaniel I. Durlach, Dave Warner, Col. Richard M. Satava, M.D., Myron Krueger, Ph.D., Walter J. Greenleaf, Ph.D., Paul Cutt, Narender P. Reddy, Ph.D., Scott Hassan, Alan Barnum-Scrivener, John Peifer, M.A. TELEROBOTICS: Reach Out and Touch Something. Ian Hunter, Ph.D., Paul S. Schenker, Ph.D., Elmar H. Holler, Steven T. Charles, M.D., Bela L. Musits, Hugh Lusted, Ph.D., Janez Funda, Ph.D., Yulun Wang, Ph.D. SUBMITTED PAPERS: Gabriele Faulkner, Ph.D., Uwe G. Kuehnapfel, Ph.D., Matthias Wapler, R. Bowen Loftin, Ph.D., Jaren Parikh, Kurt R. Smith, D.Sc., Bruce Kall, M.S., Donald W. Kormos, Ph.D., David W. Cloyd, M.D., Penny Jennett, Ph.D., Lauren Gabelman, M.S., Joshua Lateiner, Anthony M. DiGioia III, M.D., Joseph B. Petelin, M.D., Timothy Poston, Erik Viirre, M.D., Ph.D., Mark Bolas, A. David Johnson, Ph.D., Brian D. Athey, Ph.D. SUNDAY, January 30 TELEMEDICINE: The Global Health Community. Dave Warner, Michael F. Burrow, Jay H. Sanders, M.D., Ralph Martinez, Ph.D., William J. Dallas, Ph.D., John D. Hestenes, Ph.D., Rudy Mattheus, M.Sc., Georges J.E. De Moor, M.D., Jens P. Christensen, M.SE., MBA SUMMARY DISCUSSION: Improving Quality, Continuity, and Access to Healthcare While Reducing Cost. Faina Shtern, M.D., Col. Richard M. Satava, M.D., Makoto Nonaka, M.D., Ph.D., Nathaniel I. Durlach, John D. Hestenes, Ph.D., Rudy Mattheus, M.Sc., Melvyn Greberman, M.D., MPH EXHIBITS: Advanced Visual Systems, Inc., Artma Biomedical, Inc., BioControl Systems, Inc., Computer Motion, Inc., Dimension Technologies, Inc., Engineering Animation, Inc., XTensory, Inc., High Techsplanations, Inc., Image Technology Associates, Inc., Immersion Corp., IVI Publishing, IXION, Kaiser Medical Optics, Inc., Shooting Star Technology, Silicon Graphics, Inc., SONY Medical Systems, Inc., Stealth Technologies, Inc., Pixys, Inc., Virtual Vision From arne@ewald.mbi.ucla.edu Mon Dec 20 13:57:45 1993 Received: from ewald.mbi.ucla.edu for arne@ewald.mbi.ucla.edu by www.ccl.net (8.6.4/930601.1506) id NAA13854; Mon, 20 Dec 1993 13:16:35 -0500 Received: by ewald.mbi.ucla.edu (5.57/Ultrix3.0-C) id AA28085; Mon, 20 Dec 93 10:16:09 -0800 Date: Mon, 20 Dec 93 10:16:09 -0800 From: arne@ewald.mbi.ucla.edu (Arne Elofsson) Message-Id: <9312201816.AA28085@ewald.mbi.ucla.edu> To: CHEMISTRY@ccl.net Subject: Protein parameter format exchange? Dear Netters. Does anyone have a program that can read parameter files from different MD programs and then output them into any format ? This would be very usefull for comparing different force-fields. I realize that there must be some problems when doing this but i guess these could be taken care of manually. please respond to me by email and I summarize arne@escher.mbi.ucla.edu From hugo@montara.molres.org Mon Dec 20 14:06:54 1993 Received: from mail.barrnet.net for hugo@montara.molres.org by www.ccl.net (8.6.4/930601.1506) id NAA14218; Mon, 20 Dec 1993 13:54:16 -0500 Received: from montara.molres.org by mail.barrnet.net (5.67/1.37) id AA06649; Mon, 20 Dec 93 10:54:12 -0800 Received: by montara.molres.org. (4.1/SMI-4.1) id AA12425; Mon, 20 Dec 93 10:54:24 PST Date: Mon, 20 Dec 93 10:54:24 PST From: hugo@montara.molres.org (Hugo Villar) Message-Id: <9312201854.AA12425@montara.molres.org.> To: -u@montara.molres.org, chemistry@ccl.net Subject: Drug design Hi everyone! Several considerations on drug design at the industry. The most striking success story tome is that of the Agouron people in San Diego is sort of a textbook example. There are also several textbook failures!. Second people are not as naive as we think in the industry any more. Thanks to the work of many people they know what to expect. (I do not want to give particular names to avoid the injustice of forgetting some of these true pioneers). Most big companies have modeling efforts. Some are more commmitted to theoretical tools than others. There are companies that are based on the premise of theoretical drug design for drug discovery, such as Arris Pharmaceuticals, Vertex and Auguron. However, even the "laymen" in most companies understand enough to realize that they cannot expect all the solutions from their modeling groups. However, there is a way to check the level of enlightment of the person who is interviewing you: ask them what is that they expect from the computational chemistry/modeling groups. If the answer is the Sun and the Stars you'll be better off waiting for the next opportunity. When I asked that to my current boss the answer was: " I am aware that we can not expect a single handed solution to our drug design problems from you. However, I know that we are better off with you onboard than without someone like you." In other words, can anyone mention a drug that has been taken to the market or clinical trials because of NMR or X-Ray crystallography?. However, we are better off with them than without them. In multidisciplinary collaborative projects it is very hard to trace which is the contribution of any one field to the ultimate success of the project. I think that part of the problem lies with the use of terms like computer-aided drug design, it makes it sound too much like designing a car. Nothing further from the truth.. Sorry I got carried away. Hugo Villar ============================================================================== Hugo O. Villar, PhD. Computational Chemistry Lab. Terrapin Technologies, Inc. 750-H Gateway Blvd. South San Francisco. CA 94080. (415)244-9303. FAX: (415) 244-9388. ============================================================================== From DSMITH@uoft02.utoledo.edu Mon Dec 20 15:57:48 1993 Received: from uoft02.utoledo.edu for DSMITH@uoft02.utoledo.edu by www.ccl.net (8.6.4/930601.1506) id PAA15938; Mon, 20 Dec 1993 15:35:52 -0500 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.2-10 #3438) id <01H6PHGX14UK0003W3@UOFT02.UTOLEDO.EDU>; Mon, 20 Dec 1993 15:34:56 EST Date: Mon, 20 Dec 1993 15:34:56 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: AVS Chemistry Viewer announcement To: chemistry@ccl.net Cc: mmodinfo@uoft02.utoledo.edu Message-id: <01H6PHGX14UM0003W3@UOFT02.UTOLEDO.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: CHEMISTRY X-VMS-Cc: MMODINFO MIME-version: 1.0 Content-transfer-encoding: 7BIT The AVS Chemistry Viewer is alive and well and living in a new home. You can obtain more information through: anon.ftp/gopher www.ccl.net in /pub/chemistry/info/software-packages/AVS.info or you can get it via e-mail by sending a message: select chemistry get info/software-packages/AVS.info to MAILSERV@ccl.net or by contacting: Douglas A. Smith, Ph.D. President DASGroup voice: 419-537-2116 or 419-472-9160 fax: 419-537-4033 email: dsmith@uoft02.utoledo.edu mailing address: 3807 Elmhurst Road Toledo, OH 43613-4209 From BLANKENS@CPWSCA.PSC.EDU Mon Dec 20 16:58:07 1993 Received: from CPWSCA.PSC.EDU for BLANKENS@CPWSCA.PSC.EDU by www.ccl.net (8.6.4/930601.1506) id QAA16634; Mon, 20 Dec 1993 16:10:05 -0500 Date: Mon, 20 Dec 1993 16:09:42 -0500 (EST) From: BLANKENS@CPWSCA.PSC.EDU To: chemistry@ccl.net CC: MMADRID@CPWSCA.PSC.EDU, BLANKENS@CPWSCA.PSC.EDU Message-Id: <931220160942.2021a79c@CPWSCA.PSC.EDU> Subject: Posting PSC Supercomputing Training Workshop We would appreciate your posting on your supercomputing network the following Pittsburgh Supercomputing Center biomedical training workshop. Thank you, Nancy Blankenstein May 29-June 3, 1994 Nucleic Acid and Protein Sequence Analysis Supercomputing Training Workshop for Biomedical Researchers Pittsburgh Supercomuting Center Application deadline: March 31, 1994 Contact: Nancy Blankenstein, 412-268-4960 or blankens@psc.edu