From mgw@stan.xx.swin.OZ.AU Thu Jun 17 13:35:26 1993 From: mgw@stan.xx.swin.OZ.AU (Margaret Wong) Message-Id: <9306170835.AA11454@stan.xx.swin.OZ.AU> Subject: amino acid sequence searching To: chemistry@ccl.net Date: Thu, 17 Jun 93 18:35:26 EST Sorry to send this to the net but it bounced when sent to the originator Hi, If you want to get information on lots of helpful things on the embl-server send some email to NETSERV@EMBL-Heidelberg.DE FASTA@EMBL-Heidelberg.DE quick@EMBL-Heidelberg.DE blitz@EMBL-Heidelberg.DE PredictProtein@EMBL-Heidelberg.DE all with no subject and a one line message HELP which will bring you back lots of very useful info on how to use and access various facilities such as sequence searching Margaret Wong (mgw@stan.xx.swin.oz.au or marg@chem1.chem.swin.oz.au) From GOVENDEM@che.und.ac.za Mon Jun 17 16:32:59 1993 Message-Id: To: Chemistry@ccl.net From: GOVENDEM@che.und.ac.za Date: 17 Jun 93 14:32:59 +0200 (SAST) Subject: re: g92 MULTIPLICITY=2 PROBLEM. Hi; S O S S O S S O S. I'm not very sure if this is a correct forum. I will pose the quetion anyway. I tried frequency jobs with Nitric Oxide (multiplicity=2). The theoretical value is 3915 wavenumbers, this is about twice experimental one. PROBLEM 1 The other systems with multiplicity=1 do not pose such a problem. With Nitrogen dioxide also multiplicity=2, the calculation on frequencies just won't proceed, i.e crashes by exceeding normal 65 cycles. PROBLEM 2 Now the question is this? Has anyone out there, encountered these problems on Gaussian 92 in Unix system? Please help. Thanks in advance; TM Tshehla. TAKING A BOY TO COLLEGE MAKES HIS LIFE MISERABLE !!! From ssidner@karplus.unmc.edu Thu Jun 17 03:05:49 1993 Date: Thu, 17 Jun 93 08:05:49 CDT From: ssidner@karplus.unmc.edu (Steve Sidner) Message-Id: <9306171305.AA11207@karplus.unmc.edu> To: chemistry@ccl.net Subject: Re: CCD e-mail The Cambridge Structural Database (CSD) is only available by license >from Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K. Attn: Dr. Olga Kennard F.R.S. In the U.S.A., licenses are available from the Medical Foundation of Buffalo, 73 High St., Buffalo, N.Y., 14203-1196, Attn: Ms. Phyllis Strong. It is available for several popular machines. Currently, it requires approximately 300 MB of disk space. Steve Sidner Eppley Institute, University of Nebraska Medical Center 600 S. 42nd St., Omaha, NE, 68198-6805, U.S.A. (402) 559-4921, FAX: (402) 559-4651 ssidner@unmc.edu ssidner@unmcvm.bitnet From rwoods@biop.ox.ac.uk Thu Jun 17 15:40:41 1993 Date: Thu, 17 Jun 1993 14:40:41 +0100 From: rwoods@biop.ox.ac.uk To: chemistry@ccl.net Message-Id: <0096E2A5.D73BCC60.4146@biop.ox.ac.uk> Subject: Simulated Annealing using Sander Dear Netters, I have been trying to set up a simulated annealing run with Amber4.0 using the Sander module. So far without success. I am trying to heat the system to 2000 K then cool it in 50 K steps (of 1ps each) to 300 K. Then hold it at 300 K for a 50 ps MD run. I would be very greatful to anyone for a copy of a suitable input file. There is a sample input in the Amber demo files, but it is too basic for my purposes. Thanks very much, Rob Woods Robert J. Woods, Ph.D. Glycobiology Institute Department of Biochemistry University of Oxford South Parks Road Oxford, OX1 3QU From wcg@ussu.Ciba.Com Thu Jun 17 13:29:03 1993 Date: Thu, 17 Jun 1993 17:29:03 -0400 From: wcg@ussu.ciba.com (Wayne C. Guida) Message-Id: <9306172129.AA10805@pharma.ussu.Ciba.Com> To: CHEMISTRY@ccl.net Subject: Successful Examples of Rational Drug Design Dear Netters, There has been some conversation recently concerning examples in which computational methods have been used successfully for rational drug design. Mark Smythe (mls@wucmd.wustl.edu) writes: >mike whitbeck (whitbeck@maxey.unr.edu) writes: > >...(deleted parts of message) > >I recall awhile back there was some traffic about 'has comp. chem. methods >ever developed a new drug ?' I no longer recall the consensus of that >conversation (or was it on the drug discovery list out of oz?). >If anyone recalls a concrete example where the calculations made the >difference tell us about it. > >...(deleted parts of message) ...(deleted parts of message) I would like to point out that there are several examples of structure-based drug design in which computational methods in conjunction with protein crystallographic methods have PROVEN to be successful in the design of enzyme inhibitors that have therapeutic utility. The most recent example is the one Mark Smythe referred to in his recent email, and which appeared in Nature, 363, 418-423 (1993). This work involves the rational design of sialidase inhibitors for treatment of influenza. Note that the therapeutic value in man has yet to be demonstrated. In their excellent chapter in Annual Reports in Medicinal Chemistry (Chapter 29 - "Macromolecular X-ray Crystallography and NMR as Tools for Structure-based Drug Design", Volume 27, 1992, Academic Press), John Erickson and Stephen Fesik cite several additional earlier examples (though the emphasis is on X-ray and NMR). In their article they describe the iterative design of thymidylate synthase (TS) inhibitors by the group at Agouron Pharmaceuticals as well as our work (a collaborative effort between Ciba and Biocryst Pharmaceuticals) on the iterative design of inhibitors of Purine Nucleoside Phosphorylase (PNP). In both cases computer assisted molecular modeling definitely played a critical role. I believe that Agouron has at least one TS inhibitor in clinical trials and Biocryst has reported successful Phase I/II clinical trials for BCX-34, a PNP inhibitor that was discovered as a result of the structure-based drug design effort mentioned above. For references to our work on PNP inhibitors, see: Ealick, et. al., Proc. Natl. Acad. Sci. USA, 88, 11540 (1991) for the "Readers Digest" version and Montgomery, et. al., J. Med. Chem., 36, 55-69 (1993) for paper #1 of a series of J. Med. Chem. papers that are either in press, submitted, or in preparation. -Wayne C. Guida ========================================================================= Wayne C. Guida Pharmaceuticals Division Ciba 556 Morris Ave. Summit, New Jersey 07901 Phone: 908-277-7954 Internet: wcg@ussu.ciba.com ========================================================================= From matt@mercury.aichem.arizona.edu Thu Jun 17 10:37:31 1993 Date: Thu, 17 Jun 1993 17:37:31 -0700 (MST) From: Matthew Stahl Subject: animation To: chemistry@ccl.net Message-Id: Hello Netters, I am wondering how many of you have used animation as a teaching or research tool. What platforms and software are available to do this sort of thing besides Cache? If you had the ability to make an animation on a PC by stringing together coordinate files (like Macromodel or Xmol) what would you want to display? Dynamics simulations? Gaussian vibrational modes? Reaction Mechanisms? Would the ability to do this on a PC be useful? Thanks in advance. Responses will be summarized and posted if this topic generates sufficient interest. ******************************************************************** ** ** ** *** DEPARTMENT OF CHEMISTRY ** ** ** ** ** ** ARTIFICIAL INTELLIGENCE IN CHEMISTRY ** ** ** ** ******* matt@mercury.aichem.arizona.edu ** ** ***** ** ** MATTHEW STAHL ** ********************************************************************