From chemistry-request@ccl.net Thu Jul 18 02:39:45 1991 Date: Wed, 17 Jul 91 21:13 CST From: MARTIN%cmda.abbott.com@RELAY.CS.NET Subject: Two Symposia on 3D Modeling, etc at the Fall 1991 ACS Meeting in NY To: CHEMISTRY%ccl.net@RELAY.CS.NET Status: R Symposia of Interest at the American Chemical Society Meeting in New York August 26-30, 1991 (Registration Information in Chemical & Engineering News, June 17, 1991) Herman Skolnik Award Symposium Honoring W. T. Wipke: New Dimensions in Chemical Information Tuesday 27 August 14:00 INVENTION: A SYSTEM FOR INVENTING MOLECULAR STRUCTURES. W. T. Wipke, M. C. Pitman, R. T. Koehler, B. S. Kislin, G. D. Anderson 14:55 AUTOMATED LEARNING IN CONFORMATIONAL ANALYSIS - WIZARD III. D. P. Dolata, P. J. Walters 15:40 AN AUTOMATIC METOHD FOR THE ALIGNMENT OF MOLECULAR STRUCTURES: OPTIMIZING THE OVERLAP OF ATOM BASED PROPERTIES, IN PARTICULAR THE STERIC AND ELECTROSTATIC FEATURES. G. M. Smith, S. K. Kearsley 16:20 PHARMACOPHORE EXPLORATION. M. Hahn __________________________________________________________ Symposium on Three-Dimensional Chemical Structure Handling Wednesday 28th August 3D Searching Algorithms Y. Martin, Presiding 08.30: Prioritizing the "Hits" from a 3D Search. Robert S. Pearlman 09.05: Integrated 3D Search Facilities for the Cambridge Structural Database (CSD) F. H. Allen, O. Johnson, O. Kennard, R. S. Rowland, E.M. Mitchell, D. Watson 09.30: DATABASE STRUCTURE AND SEARCHING IN MACCS-3D. B. D.Christie, D. R. Henry, T. E. Moock 09.55: Comparison of Atom-by-atom 3D Search Routines for Searching. CAS Registry Substances. K. Cross Conformational Flexibility 10.20: The Use of Most Restrictive Paths in 3D Search Strategy. J. Bradshaw, E. G. Maliski 10.45: Flexible Queries in 3D Searching: Techniques in 3D-Query Formulation. O. F. Guner, D. R. Henry, T. E. Moock, R. S. Pearlman 11.10: Looking for Pharmacophores in 3-D Databases: Does Conformational Searching Improve the Yield of Actives? K.S. Haraki, R. P. Sheridan, A. Rusinko III, R. Venkataraghavan, D. A.Dunn, D. McCulloch 11.35: Searching 3D Databases of Conformationally Flexible Molecules: A flexible Pre-screening Technique T. Hurst, G. B.Smith, R. W. Homer, J. L. Epplin, F. Soltanshahi 12.00: A Distance Geometry-based Approach for Docking Conformationally Flexible Molecules from 2D or 3D-Chemical Databases. J. Blaney Processing of Macromolecules R. Sheridan, Presiding 14.00: A Modelling Environment for Map Interpretation T. A.Jones, J.-Y. Zou, M. Kjeldgaard 14.35: A PROLOG Approach to Integrating Protein Sequence and Structure Data G.J. Barton, C. J. Rawlings 15.00: THE PROTEIN DATA BANK - PRESENT STATUS AND FUTURE PLANS T.F. Koetzle, E. E. Abola, F. C. Bernstein, J. A. Callaway, J. J. Christian, B. R. Deroski, P. A. Esposito, A. Forman, J. E. McCarthy, J. G. Skora 15.25: The IDITIS Relational Database of Protein Structure S. P.Gardner, J. M. Thornton Database Creation and Conformational Analysis 15.50: Experiences Building the Chapman and Hall Directionary of Drugs K. Davies, R. Upton 16.15: WIZARD-III Recent Developments in AI in Conformational Analysis D. P. Dolata 16.40: Automated Conformational Analysis A. R. Leach , A. S.Smellie 17.05: Automatic Generation of 3D-Atomic Coordinates for Organic Molecules J. Gasteiger, C. Hiller, C. Rudolph, J. Sadowski Thursday 29th August Applications - I W. T. Wipke, Presiding 08.30: Recent Advances in Molecular Docking. I. D. Kuntz, B. Shoichet, D. Bodian, D. Roe, R. Lewis, C. Huang, T. Ferrin, R. Langridge 09.05: A New Method for the De Novo Design of Enzyme Inhibitors .H. J. Bohm 09.30: Discovery of Novel Inhibitors of HIV-1 Protease by Three- dimensional Substructure Searching M. G. Bures, J. W. Erickson 09.55: Docking Ligands into Receptors: the Test Case of a- chymotrypsin K. Stewart, J. Bentley, M. Cory 10.20: 3D-Shape Fitting and 3D-DB Searching by SPERM V. J. van Geerestein, P. D. J. Grootenhuis, C. A. G. Haasnoot Similarity Measures 10.45: Characteristics of Computer-Generated 3D and Related Molecular Property Data for CAS Registry Substances. W. Fisanick 11.10: Measures of 3D Shape Similarity. P. G. Mezey 11.35: Implementation and Use of an Atom-mapping Procedure for Similarity Searching in Databases of 3-D Chemical Structures. C.A. Pepperrell, P. Willett R. Taylor Applications - II P. Willett, Presiding 14.00: CAVEAT; a Vector-Based Approach to Computer-aided Molecular Design P. A. Bartlett, G. T. Shea, S. Waterman, S. J. Telfer 14.35: Knowledge Acquisition from Crystallographic Databases. F.H. Allen, R. S. Rowland, S. Fortier, J. I. Glasgow 15.00: Building 3D Structural Databases: Experiences with MDDR-3D and FCD-3D. D. R. Henry, P.J. McHale, B. D. Christie, D.Hillman 15.25: Using Databases as an Aid in Developing Synthetic Targets C. J. Eyermann, P. Y.-S. Lam, J. S. Kerr, Wm. C. Ripka 15.50: Automated Structure Design in 3D Valerie J Gillet, K. Flanagan, P. A. Johnson, C. Marshall, P. Mata, S. Sike, A. L. Stebbings 16.15: Experiences with Automated 3D Design of Bioactive Molecules Y. C. Martin, C. T. Lin, P. Pavlik 16.40: 3D Database Searching vs. de novo Construction: Two Complementary Methods with the Same Goal W. J,Howe, J, B. Moon Call, Email, or FAX us if you have questions. CO-CHAIRS of Symposium on Three-Dimensional Chemical Structure Handling Yvonne C. Martin Computer Assisted Molecular Design Project, D-47E Abbott Laboratories, AP9A-LL Abbott Park, IL 60064, USA TEL (708)937-5362 FAX (708)937-2625 BITNET MARTIN%CMDB.ABBOTT.COM@RELAY.CS.NET Peter Willett Department of Information Studies University of Sheffield Sheffield, S10 2TN, England TEL (742)768555 ext. 6113 FAX (742)739826 BITNET: LI1PBW%SHEFFIELD.PRIMEA%NSS.CS.UCL.AC.UK@RELAY.CS.NET JANET: LI1PWB@UK.AC.SHEFFIELD.PRIMEA From jkl@ccl.net Thu Jul 18 11:29:04 1991 To: chemistry@ccl.net Subject: New kinetics software from Mike Whitbeck Date: Thu, 18 Jul 91 11:31:07 EDT From: jkl@ccl.net Status: R Thanks to Mike Whitbeck from Desert Research Institute, we have now an enhanced version of his REACTION program which deals with the kinetics of the set of chemical reactions. This is now version 2. The stiff-diferential-equations' solver lsoda is unchanged from previous version, but the REACT part now allows you also to fit rate parameters. The examples were added, too. How to get more info about the program: Send following line to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET: send kinetics2/react/docs/readme from chemistry The file with more description will be automatically sent to you. How to get the program and test data: a) People with ftp cd to_the_directory_you_want_kinetics_program_to_be ftp www.ccl.net (or ftp 128.146.36.48) Login: anonymous Password: your_email_address ftp> cd pub/chemistry/kinetics2 ftp> ls ftp> get readme ftp> binary ftp> get react2.tar.Z ftp> quit Then you uncompress and untar the react2.tar.Z as: zcat react2.tar.Z | tar xvof - (if your UNIX does not allow "o" option in tar, you need to be a root). You can also get individual, uncompressed files (e.g., if you are on the VAX and do not have tar and zcat) by going down the directory tree starting from pub/chemistry/kinetics2. b) If you do not have ftp, then you are left with our e-mail interface. You obtain instruction on how to get REACT by e-mail by sending a message: send kinetics2/oscpostfile from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET or OSCPOST@oscsunb.ccl.net Jan Labanowski, Ph.D (Ph.D. - means: Low pH in Duodenum) Ohio Supercomputer Center jkl@ccl.net From jkl@ccl.net Thu Jul 18 12:13:51 1991 To: chemistry@ccl.net Subject: Newer version of MindTool available Date: Thu, 18 Jul 91 12:15:56 EDT From: jkl@ccl.net Status: R There is a newer version of MindTool (a molecular graphics software) available. It is dated Jun 25, 1991. You can get it by ftp either from www.ccl.net [128.146.36.48] or from rani.chem.yale.edu [130.132.25.65]. The authors are: Jim Blake Julian Tirado-Rives from Yale University. To find more, read the README file. To get it: cd to_the_directory_where_you_want_files_of_MindTool ftp machine_name_or_number login: anonymous Password: your_email_address ftp> binary ftp> prompt ftp> cd pub/MindTool ftp> ls -l ftp> mget * ftp> quit The README file tells you what to do. The mind file is an executable for SparkStation. The mindtool.tar.Z file is a source, example, docs, etc. and needs to be uncompressed as zcat mindtool.tar.Z | tar xvof - You might need to be a root to do it. Unfortunately, the program is too large, to go via e-mail interface. Jan Labanowski Ohio Supercomputer Center jkl@ccl.net