From ZSYAMP01%EBCESCA1.BITNET@phem3.acs.ohio-state.edu Fri Jul 23 11:32:32 1993 Date: Fri, 23 Jul 1993 10:32:32 +0100 (CET) From: ZSYAMP01%EBCESCA1.BITNET@phem3.acs.ohio-state.edu Subject: Chem-X To: chemistry@ccl.net Message-Id: <01H0VCDHBFR68WWH9J@phem3.acs.ohio-state.edu> I want to thank all the people who replied to my query about Chemical Design Ltd. address. I'm literally overflown with the answers. Anyway, when I said 'it looks as if it never existed' I just meant that I couldn't find Chem-X in the Directories of Applications for CRAY, IBM and Silicon computers. It wasn't my purpose to hurt anybody's feelings. Thanks again. Alicia ------------------------------------------------------------------------ Alicia Martinez Supercomputation Center of Catalonia (CESCA) Phone: (34)(3) 4914014 Avda. Diagonal 645 Fax: (34)(3) 4904635 08028 Barcelona BITNET: ZSYAMP01@EBCESCA1 SPAIN Internet: zsyamp01@puigmal.cesca.es ------------------------------------------------------------------------ From tom@sgih.roc.wayne.edu Fri Jul 23 06:11:58 1993 Message-Id: <9307231413.AA21121@sgih.roc.wayne.edu> Date: Fri, 23 Jul 1993 10:11:58 -0400 To: chemistry@ccl.net From: tom@sgih.roc.wayne.edu (Tom Wiese) Subject: Display PBD files on Mac? Hello All, Does anybody know of a public domain software that one could use to view and do basic manipulations of PDB files on a Mac? I am looking particularly for something simple and easy that undergraduate students could use to explore basic features of protein structure. If there is a fairly low cost commercial package that will do this on a Mac, I would like to know about it as well. Thanks in advance, Tom ################################################## Tom Wiese Department of Biochemistry Wayne State University School of Medicine 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-5605 FAX: (313) 577-2765 email: tom@sgih.roc.wayne.edu ################################################## From chris@glycob.ox.ac.uk Fri Jul 23 11:16:20 1993 Date: Fri, 23 Jul 1993 15:16:20 EDT From: chris@glycob.ox.ac.uk To: CHEMISTRY@ccl.net Message-Id: <0096FEF4.C8F3E1E0.6822@glycob.ox.ac.uk> Subject: QSAR Hello netters, I am looking for a good QSAR program. I would be interested in hearing from anyone who has made a comparison between the different programs available. Please reply to me personally. Thank you for your help. *************************************************************** * Dr. Chris. Edge * Tel. +44-865-275-338 * * Glycobiology Institute * Fax. +44-865-275-216 * * Oxford University * e-mail chris@glycob.ox.ac.uk * * South Parks Road * 100117.3646@compuserve.com * * Oxford OX1 3QU U.K. * * *************************************************************** From raman@bioc01.uthscsa.edu Fri Jul 23 07:00:18 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9307231700.AA07301@bioc01.uthscsa.edu> Subject: Protein Conformation calculation To: chemistry@ccl.net Date: Fri, 23 Jul 1993 12:00:18 -0500 (CDT) Chuck: > In the next few weeks we will be starting a project to predict a > structure for a protein that has not been crystalized. I'm interested Predicting the structure of a protein from the amino acid sequence is now a field by itself and there are a lot of techniques being applied to improve the quality of prediction, e.g. neural networks. However, the following citation is the most interesting. Steven Benner's group was challenged to predict the structure of Src-homology 3 domain by a group of crystallographers who had just solved the crystal structure. How well did the predicted structure fair with the crystal structure? I will let you be the judge after reading the article. 1. Nature (Lond.) [1992] 359, 781 Correct Structure prediction (and references therein). 2. ibid. [1992] 359, 851 Crystal structure of src Hom. 3 domain 3. Benner, S.A., et al.[1993] J. Mol. Biol. 229, 295-305 4. Benner, S. A. [1993] FEBS Lett. 325, 29-33 5. Sander, C [1992] 360, 540 Jury returns on Structure prediction (an evaluation of how well Benner's prediction did) 6. Sander, C. [1993] TIBS 18, 120-123 Review on the current status of structure prediction. This should get you started on your problem. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From mwd@carina.cray.com Fri Jul 23 07:31:51 1993 From: mwd@carina.cray.com (Mark Dalton) Message-Id: <9307231731.AA11648@calamity> Subject: 3D substructure searching To: chemistry@ccl.net Date: Fri, 23 Jul 93 12:31:51 CDT Hi! Does anyone know of a program that will take a known 3D structure or substructure and be able to search the PDB for similar 3D structures or substructures? Or even search a substructure against a single structure? I don't think the MULTI package does what I need, I think that will take a predict the structure of a unknown structure by comparing the primary sequence with a known structure, or a profile of substructures. Any information would be appreciated. Thanks! Mark -- Mark Dalton AUG-GCU-AGA-AAG H Cray Research, Inc. M A R K | Eagan, MN 55121 CH3-S-CH2-CH2-C-COOH Internet: mwd@cray.com | (612)683-3035 NH2 From raman@bioc01.uthscsa.edu Fri Jul 23 08:20:15 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9307231820.AA07425@bioc01.uthscsa.edu> Subject: Display PDB files on Mac... To: chemistry@ccl.net Date: Fri, 23 Jul 1993 13:20:15 -0500 (CDT) Tom Try the program called KINEMAGE, which is now distributed with every issue of Protein Science and available via anon. FTP sites as well. I have include a brief description of the kinemage.readme file. You can ftp to "fly.bio.indiana.edu" and look in the directory /chemistry/mac for kinemage.hqx ************************** A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. MAGE is a display program, which presently runs on Macintosh and PC computers, to view and explore kinemages. An early version of MAGE is briefly described in the Richardson & Richardson article in the first issue of Protein Science (Jan. '92). The kinemage format is defined in that article, and although there are now more keywords and parameters, the basic definitions have been stable. PREKIN is a utility program which prepares trial kinemages from Brookhaven Protein Data Bank format coordinate files. An early version is briefly described in the Richardson & Richardson article in the first issue of Protein Science (Jan. '92). These demo kinemages are included with the software: Demo2_2a.kin "THE KINEMAGE: A TOOL FOR SCIENTIFIC COMMUNICATION" D. Richardson and J. Richardson Reader's tutorial: Kin.1 - Carboxypeptidase active site motions (basic operations, IDs, animation) Kin.2 - Carbonic anhydrase, Calphas and active site (zoom, stereo) Kin.3 - Carbonic anhydrase, closeup of loop (centering, unpickable points) Kin.4 - Leucine zipper structure (zoom, slab, ztrans) Kin.5 - Alpha helix (measures, drawline) Demo2_2b.kin "THE KINEMAGE: A TOOL FOR SCIENTIFIC COMMUNICATION" Further examples for authors: Kin.1 - Palette of colors available in MAGE Kin.2 - Format example of a kinemage file Kin.3 - NMR NOE data: BPTI PalphaPbeta Kin.4 - Phi vs Psi vs Chi1 plot for phenylalanine Kin.5 - Helix-helix contact, rows i,i+3 and j,j+4 The home archive for this software is via anonymous ftp to orion.oac.uci.edu in folder /protein/Kinemage -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From ipcakc@vigyan.ernet.in Tue Jul 23 17:17:25 1993 To: CHEMISTRY@ccl.net Subject: CADPAC manual Date: 23 Jul 93 22:17:25 EST (Fri) From: ipcakc@vigyan.iisc.ernet.in Message-Id: <9307232217.AA09606@vigyan.iisc.ernet.in> Will anybody send me the xerox copy the CADPAC (ab initioprogram) manual? D.sengupta India. ipcakc@ipc.iisc.ernet.in From ipcakc@vigyan.ernet.in Tue Jul 23 17:21:51 1993 To: CHEMISTRY@ccl.net Subject: Transition state opt. in CADPAC Date: 23 Jul 93 22:21:51 EST (Fri) From: ipcakc@vigyan.iisc.ernet.in Message-Id: <9307232221.AA09675@vigyan.iisc.ernet.in> Hi, Will you please inform me what are the keywords necessary for the transition state optimisation in CADPAC ( ab inition program)? Please send me a sample input file. D. sengupta India. ipcakc@ipc.iisc.ernet.in From nauss@ucmodl.che.uc.EDU Fri Jul 23 12:49:03 1993 Date: Fri, 23 Jul 1993 16:49:03 -0400 From: nauss@ucmodl.che.uc.EDU (Jeffrey L. Nauss) Subject: Modeling of Lanthanide Solutions and Complexes To: CHEMISTRY@ccl.net Message-Id: <9307232049.AA16319@ucmodl.che.uc.edu> Good day, netters - A group here at UC are considering the feasiblity of modeling La+3 (a lanthanide 3+ cation) in a saturated salt solution and in a complex with certain polysaccharides. The program which we will use for the molecular dynamic simulation is Discover with the graphical interface Insight. Obviously, we first need to set up parameters for the La ion. Anyone have any experience, references, or recommendations for approaching this project? Thank you for your time. Jeff Nauss **************************************************************************** * Dr. Jeffrey L. Nauss * telephone: 513-556-0148 or 9200 * * Director, Molecular Modeling Services * Fax: 513-556-9239 * * Department of Chemistry * * * University of Cincinnati * e-mail: nauss@ucmodl.che.uc.edu * * Cincinnati, OH 45221-0172 * or nauss@ucchem.oa.uc.edu * ****************************************************************************