From microsim@nis.net Thu Oct 3 00:56:38 1996 Received: from maple.nis.net for microsim@nis.net by www.ccl.net (8.7.5/950822.1) id AAA06504; Thu, 3 Oct 1996 00:38:17 -0400 (EDT) Received: from FORCE by maple.nis.net with smtp (Smail3.1.28.1 #2) id m0v8fV9-0010oZC; Thu, 3 Oct 96 00:35 EDT Message-ID: <32536DF2.1A70@nis.net> Date: Thu, 03 Oct 1996 00:40:34 -0700 From: Willie Cui Organization: MicroSimulations X-Mailer: Mozilla 2.02E-KIT (Win95; U; 16bit) MIME-Version: 1.0 To: Shaomeng Wang CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:Motif software! References: <199610022115.RAA28787@helix.nih.gov> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I vaguely remember that Prof. Janet Thornton published a series paper on protein motif and developed some software for this. I believe Oxford Molecular Group markets her software under the name Idditis. Check their web site. Shaomeng Wang wrote: > > Dear CCL friends, > > Could any provide me the information on the software/database for > searching for known protein motifs? > > I appreciate very much your information. > > Shaomeng Wang, Ph.D. > Georgetown University Medical Center > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: shaomeng@helix.nih.gov > -- Original Sender From: Address: shaomeng@helix.nih.gov > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html -- Willie Cui, Ph.D. voice: (201)512-0486 MicroSimulations fax: (201)512-0489 478 Green Mountain Road info@microsimulations.com Mahwah, NJ 07430 http://www.microsimulations.com From bauer@organik.uni-erlangen.de Thu Oct 3 12:57:01 1996 Received: from faui45.informatik.uni-erlangen.de for bauer@organik.uni-erlangen.de by www.ccl.net (8.7.5/950822.1) id MAA11053; Thu, 3 Oct 1996 12:34:49 -0400 (EDT) Received: from derioc1.organik.uni-erlangen.de (derioc1.organik.uni-erlangen.de [131.188.128.1]) by uni-erlangen.de with SMTP id SAA00077 (8.7.6/7.5c-FAU); for ; Thu, 3 Oct 1996 18:34:45 +0200 (MET DST) Received: (from bauer@localhost) by organik.uni-erlangen.de id RAA09667 (8.6.12/7.4f-FAU);; Thu, 3 Oct 1996 17:34:33 +0100 From: Walter Bauer Message-Id: <199610031634.RAA09667@derioc1.organik.uni-erlangen.de> Subject: NMR FID sounds To: chemistry@www.ccl.net (computational chemistry list) Date: Thu, 3 Oct 1996 17:34:32 +0100 (MET) Cc: bauer@organik.uni-erlangen.de (Walter Bauer) X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Dear netters: some of you may recall that soon after the commercial introduction of FT-NMR in the early seventies it was possible to do an auditory exami- nation of FIDs. Unfortunately, these facilities virtually became out of fashion. I have now undertaken an effort stimulate a renaissance of listening to FID sounds. Auditory monitoring of FIDs may be highly informative in certain cases. Valuable informations may be obtained from the FID sounds. In some cases the auditory information may reveal errors, e.g. in phase cycling schemes of 2D NMR spectra or in the parameter setup of a measurement. I have written an article designed for the World Wide Web on the audi- tory presentation of FIDs which may be looked up under http://www.organik.uni-erlangen.de/research/NMR/music.html (Germany mirror site) or http://paul.chem.uga.edu/www.wbauer/music.html (US mirror site) The title of the article is: "NMR meets MUSICIANS". You will be pro- vided there with detailed information of how to get FID sounds out of an NMR spectrometer. Sound files of FIDs along with visual material are provided. In addition, it is demonstrated how to play entire songs (!) on an NMR spectrometer. In order to listen to the FID sounds your WWW browser and your hard- ware must be equipped with appropriate audio facilities. The article was prepared on a Silicon Graphics Indigo workstation under IRIX 5.3. However, I have tried to make the sounds accessible to a more gene- ral public. Hence, the sounds are available both as .aiff and as .wav files. The graphics presented in the article are based on the usual .gif, .jpg, and .xbm formats. I would be very grateful receiving your comments. Have fun! Best regards to all, Waldi Bauer ******************************************************************************** Priv.-Doz. Dr. Walter Bauer * Phone: +49-9131-852987 Institute of Organic Chemistry * FAX: +49-9131-859132 University of Erlangen-Nuremberg * e-mail: bauer@organik.uni-erlangen.de Henkestrasse 42 * URL: http://www.organik.uni-erlangen. D-91054 Erlangen * de/research/NMR/Bauer.html Germany * ******************************************************************************** From mikha001@maroon.tc.umn.edu Thu Oct 3 14:56:46 1996 Received: from mhub1.tc.umn.edu for mikha001@maroon.tc.umn.edu by www.ccl.net (8.7.5/950822.1) id OAA11731; Thu, 3 Oct 1996 14:11:04 -0400 (EDT) Received: from maroon.tc.umn.edu by mhub1.tc.umn.edu; Thu, 3 Oct 96 13:11:05 -0500 Received: by maroon.tc.umn.edu; Thu, 3 Oct 96 13:11:05 -0500 Date: Thu, 3 Oct 1996 13:11:04 -0500 (CDT) From: Dmitri V Mikhailov To: chemistry@www.ccl.net Subject: docking strategy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings everyone, We are trying to do docking analysis for a system composed of a negatively charged ligand and a basic protein. We are using the Affinity module from MSI which allows flexible docking. Could someone please point out reference(s) on general strategies how to incorporate explicit solvent molecules in such a system and analyze binding energies for different ligand conformations. Thank you. Regards, Dmitri Mikhailov Ph.D. student ***************************************************** Univ. of Minnesota Medical School Department of Biochemistry Box 609, 420 Delaware St. SE Minneapolis MN 55455 tel. (612) 624-7107 fax. (612) 626-2325 e-mail: mikha001@maroon.tc.umn.edu *****************************************************