From chemistry-request@ccl.net Fri Oct 18 12:54:27 1991 Date: Fri, 18 Oct 1991 12:40:10 -0400 (EDT) From: BIOTERA@SCRI1.SCRI.FSU.EDU (Structural Biology Workshop) Subject: Computational Structural Biology Workshop *2nd Announcement To: chemistry@ccl.net Status: R ************************************************************* * SECOND ANNOUNCEMENT * ************************************************************* HIGH PERFORMANCE COMPUTING AND GRAND CHALLENGES IN STRUCTURAL BIOLOGY January 24 - 27, 1992 Florida State University Tallahassee, Florida SPONSORS: Supercomputer Computations Research Institute (SCRI) and The Structural Biology Program Florida State University ORGANIZERS: Paul A. Bash and Hagai Meirovitch The aim of the workshop is to bring together the leading scientists from academia, industry, and government agencies to discuss the role of large-scale parallel computing in Theoretical Structural Biology. The scientific focus of the workshop will be on structure/function relations in biological macromolecules such as proteins and nucleic acids and will include: (1) structure determination and the protein folding problem, (2) molecular recognition / drug design, and (3) catalysis, i.e. enzyme reaction mechanisms and electron/proton transfer processes. For additional information, contact Patricia Meredith, Conference Coordinator, at 904/644-1866, or electronically to meredith@scri.fsu.edu, or by FAX to 904/644-0098. ************************************************ * TENTATIVE PROGRAM * ************************************************ THURSDAY, JANUARY 23 7:00-9:00 PM Registraction and Reception at Cabot Lodge FRIDAY, JANUARY 24 Morning Session: PROTEIN FOLDING Chair: D.L. Beveridge F.M. Richards H.A. Scheraga M. Karplus (tentative) M. Levitt P. Wolynes Afternoon Session: PROTEIN FOLDING Chair: J. Skolnick R. L. Jernigan K.A. Dill K. Schulten Afternoon Session: GOVERNMENT AGENCIES Chair: K. Sharp DOE NIH NSF Evening Poster Session and Software Demonstration SATURDAY, JANUARY 25 Morning Session: STRUCTURE DETERMINATION Chair: W. Hendrickson H. Hauptman A.T. Brunger D. A. Case T. Havel Afternoon Session: FUTURE OF COMPUTER TECHNOLOGY Chair: B.M. Pettit B. Brooks Cray Research IBM Intel Kendall Square Research Thinking Machines Corporation SUNDAY, JANUARY 26 Morning Session: ELECTRONIC STRUCTURE Chair: M.C. Zerner W.A. Goddard III A. Warshel R. A. Friesner D. R. Salahub J.D. Joannopoulos P. Phillips Afternoon Session: MOLECULAR RECOGNITION Chair: S. Lifson J.A. McCammon B. Honig W. L. Jorgensen A. T. Hagler T. Schlick Evening Session: MOLECULAR RECOGNITION Chair: R.M. Levy R. Langridge P. Kollman MONDAY, JANUARY 27 Morning Session: DRUG DESIGN Chair: C. L. Brooks, III G. R. Marshall P. Gund Z. R. Wasserman R. E. Bruccoleri Noon Shuttle transport to Tallahassee airport ******************************************************* * GENERAL INFORMATION * ******************************************************* CONFERENCE FEE: The conference registration fee of $250 ($300 if received after December 20, 1991) will include cost of a welcome reception on Thursday, January 23rd, continental breakfasts four days, lunch three days, dinner two days, and coffee breaks daily. Registration for graduate students and postdocs is $200. We anticipate being able to provide further financial support to students and postdocs; however, this is dependent on the availability of funds at the time of the conference. REGISTRATION: A registration form is enclosed. Completed forms should be mailed to the Conference Registrar, Center for Professional Development and Public Service, Florida State University, Tallahassee, Florida 32306-2027, or FAX to (904)644-2589. Checks or money orders, in US dollars only, should be made payable to Florida State University. You may also use your Visa or Mastercard credit card to register (A 2% surcharge will be added). If you prefer to register by electronic mail, send the information requested on the registration form to meredith@scri.fsu.edu. For program information contact Pat Meredith, Conference Coordinator, at (904)644-1866 or FAX 904/644-0098. CANCELLATION: Should you find it necessary to cancel your registration, the Center for Professional Development and Public Service must receive your request for a refund in writing no later than December 20, 1991. ACCOMMODATIONS: A block of rooms has been reserved at the Cabot Lodge, 2735 North Monroe Street, Tallahassee, Florida 32303. Telephone number is (904) 386-8880, or toll-free 800-223- 1964. The negotiated rate for the conference is $54 per night, single or double. Conference participants are responsible for making their own hotel reservations directly with the hotel. Overseas participants should contact Patricia Meredith if assistance is required with making hotel reservations. When making your reservations, be sure to mention you will be attending the Structural Biology Workshop sponsored by FSU. TRAVEL: Tallahassee, the capital city of the State of Florida, is situated in the Big Bend area of North Florida and its municipal airport is served by Delta, American and USAir, as well as a number of smaller carriers. Delta Airlines and USAir have arranged special discounted fares for your travel (certain restrictions may apply). For further details regarding the Delta discount, contact Delta at 1-800-221-1212 and ask for Special Meeting Network. The reference number for this meeting is I-39039. The USAir file reference number is Gold File Number 23940005. There are no special rates for flights originating outside the United States. We remind overseas visitors that Tallahassee does not have an international airport, and it is difficult to change foreign currency even at a bank. LOCAL TRANSPORTATION: All sessions will be held at the Florida State Conference Center, 555 West Pensacola Street, Tallahassee, on the campus of Florida State University. Local transporation between the hotel and the conference center has been arranged at no additional cost. Shuttles will run morning and evening, during the conference. A local map will be provided to all registrants. POSTERS: There will be one poster session during the workshop. Please submit on one page, a camera ready abstract including key references within a text area of 16 x 24 cm to Professor J. Cioslowski, B-186 SCRI Florida State University Tallahassee, FL 32306--4052 The deadline is January 3, 1992. ************************************************************* * ELECTRONIC REGISTRATION FORM * * * * FOR STRUCTURAL BIOLOGY WORKSHOP * ************************************************************* NAME:_______________________________________SS#_________________________ STUDENT: ____ POSTDOCT _____ (Please check one if appropriate) ORGANIZATION:___________________________________________________________ MAILING ADDRESS: _______________________________________________________ ___________________________________________________________ ___________________________________________________________ ___________________________________________________________ TELEPHONE NUMBER: _______/__________________ INTERNET EMAIL ADDRESS: ____________________ FEES: $250 before December 20, 1991 $300 after December 20, 1991 $200 Graduate Students and Postdocs PLEASE CHECK ONE: I wish to pay my fee by: ____ Check (Make payable to Florida State University) [ ] MASTERCARD [ ] VISA (2% SURCHARGE ADDED) ACCOUNT #: _____________________________________ EXPIRATION DATE: _____________________________ Mail to: Conference Registrar Center for Professional Development & Public Service Florida State Conference Center R-55 Florida State University Tallahassee FL 32306-2027 or FAX this completed form to: (904)644-2589 From chemistry-request@ccl.net Fri Oct 18 16:17:47 1991 Date: Fri, 18 Oct 91 16:01:58 -0400 From: Shi Yi Yue To: chemistry@ccl.net Subject: SUM: database & software for organic compounds Status: R Dear Netters, This is a summary about "data base and software for organic compounds" I questioned four days ago. The original post includes following questions: 1) the availability of the data base of Aldrich and/or other chemical structure (3D) data base. 2) Are there any differences between this (these) data base(s) and Cambridge data base? 3) Is there any data base software available, which can be used to handle a small data base (less than 200 structures of small organic compounds), in both academic or commercial levels? 4) Is there any review article recently published about these subjects? I sould like to thank MARTIN@cmda.abbott.com (Yvonne Martin) kpc23@cas.bitnet (Kevin P. Cross) chiremv!andromeda!jeffb@uunet.UU.NET (Jeffrey Blaney) srheller@asrr.arsusda.gov (Stephen R. Hellee) for answering my questions. Here is their answers: ==== Date: Tue, 15 Oct 1991 12:56 CDT ==== From: MARTIN@cmda.abbott.com If you send me your address I will send you a reprint of an article >from Reviews in Computational Chemistry about 3D databases Y. C. Martin, M.G. Bures and P. Willett, Chapter in "Reviews in Computational Chemistry" K. Lipkowitz and D. Boyd, Eds., VCH Publishers, Inc. New York. "Searching Databases of Three-Dimensional Structures," p. 213-263, 1990. I would suggest that you look into the Daylight Chemical Information System software. They have very reasonable prices for academics and quite reasonable for industrial users. You can create your own databases and store whatever associated information you wish. We store 3D coordinates, observed and predicted bioactivities, the name of the bioactive conformation (in the list of all the coordinate sets, eg from distance geometry)... I can also send you a reprint about that: Y. C. Martin, E. B. Danaher, C. S. May, and D. Weininger, J. Computer-Aided Molec. Design.2, 15-29,1988, "MENTHOR, A Database System for Three-Dimensional Structures and Associated Data Searchable by Substructure Alone or Combined with Geometric Properties", The difference between this and Cambridge is that this is software, you supply the coordinates. In the Daylight software you have much more flexibility in what data you store and in how you search it. It is also about 2 orders of magnitude faster to do a substructure search and much easier to retrieve data. My own interest is in 3D searching, particularly in the design of molecules automatically by computer. Both our internal molecular graphics and our 3D searching software makes intimate use of the Daylight software. We also use it for atom typing for molecular mechanics. Version 3.6 is the VAX production version. I think this runs on UNIX and IBM also. Version 4 is a total rewrite in C/UNIX... It is mostly done and tremendously fast. J. H. Van Drie, D. Weininger, and Y. C. Martin, J. Computer-Aided Molec. Design, 3 225-251, 1989, "ALADDIN: An Integrated Tool For Computer-Assisted Molecular Design and Pharmacophore Recognition From Geometric, Steric, and Substructure Searching of Three-Dimensional Molecular Structures". Y. C. Martin, Chapter in "Crystallographic and Modeling Methods in Molecular Design", C. E. Bugg and S. Ealick, Eds., Springer-Verlag, New York pp 254-263, 1990 "Aladdin: A Real Tool for Structure-Based Drug Design" Y. C. Martin, Chapter in "Frontiers in Drug Research, Alfred Benzon Symposium 28", B. Jensen, F. S. J?rgensen, H. Kofod, Eds., Munksgaard, Copenhagen, pp 222-229, 1990, "Beyond Graphics: ALADDIN, A Computer Tool for Drug Design". Y. C. Martin, Tetrahedron Computer Methodology. , 3, 15-25, 1990, "Computer Design of Potentially Bioactive Molecules by Geometric Searching with ALADDIN" (invited article). If you have more questions, just ask. @@@@@@@@@@@ Yvonne Martin, Senior Project Leader @ Computer Assisted Molecular Design Project @@@@@@@@ @ D-47E, AP9A-LL @ @ Abbott Laboratories @ @ One Abbott Park Road @@@@@@@@@@ Abbott Park, IL 60064 Phone: 708 937-5362 FAX: 708 937-2625 ==== Date: Tue, 15 Oct 1991 14:54:35 -0400 ==== From: kpc23@cas.bitnet (Kevin P. Cross Ext. 3192 Room 2209B) This is not meant as an advertizement, just a response to your question. Chemical Abstracts Service currently has 3D CONCORD-generated coordinates for over 5 million (and growing) organic structures available on the STN REGISTRY file for downloading. Although 3D substructure searching of these coordinates is not available (this is a current area of research), 2D exact, substructure, and family searches can be used to find structures of interest. Those structures that are flagged as having 3D coordinates, can be downloaded in either SYBYL or ALCHEMY format. There are costs in both searching and downloading structures, however, academic discounts are available. Local 3D database searching software is available from MDL, Tripos (forthcoming), Chemical Design Ltd., and presumably, other PC-based systems. I assume you are already familiar with Cambridge's 3D search software and database. Kevin P. Cross Research Chemical Abstracts Service kpc23@cas P.S. I am NOT a marketing person. ==== Date: Tue, 15 Oct 91 14:10:45 PDT ==== From: chiremv!andromeda!jeffb@uunet.UU.NET (Jeffrey Blaney) Currently the Aldrich database is only available as part of the Fine Chemicals Database, which is sold by Molecular Design in either 2D or 3D versions. The 3D version's coordinates were generated by CONCORD - a rule-based program which generally does an excellent job at building three-dimensional low energy conformers of small organic molecules. There is, of course, a major difference between this and the CAMBRIDGE data base. The CAMBRIDGE data base contains experimentally determined X-ray crystal structures, not model-built structures. Some of the chemicals in Aldrich's database are in CAMBRIDGE, but the overlap is small. Molecular Design has chemical database software for the Mac and PC which can handle a small database. Simple chemical database software is also available from the ACS which may meet your needs. Check recent issues of C&E News, or call the Books & Journals division of ACS and ask for information about their software. I can't recall any review articles about chemical database software, but look through recent issues of J. Chem. Inf. and Comp. Sci. and you may find something. ==== Date: 15 Oct 91 21:57:00 EDT ==== From: "STEPHEN R. HELLER" FOR PC software of this type see the following article: Heller & Meyer, Chemistry International, 12, #3, pages 89-94, 1990. --------------------END OF THE SUMMARY-------------------------------- Shi-Yi Yue (514) 496-6338 shiyi@bri.nrc.ca From chemistry-request@ccl.net Fri Oct 18 18:03:58 1991 Date: Fri, 18 Oct 91 16:55:07 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) To: chemistry@ccl.net Subject: COLUMBUS Addendum Status: R ADDENDUM to the COLUMBUS Program System announcement of 14-Oct-91 (Columbus Day) If your machine cannot resolve the name ftp.tcg.anl.gov, then you can use instead the IP number 130.202.56.2 to access the COLUMBUS codes with anonymous FTP. The number may change in the future, but (to the extent possible) the name will remain the same. It should be mentioned also that the codes run on various workstations (Sun, Stardent, SGI), minicomputers (VAX), mainframes (IBM 370 and 3090), minisupercomputers (Alliant, Convex, Stardent, FPS), and supercomputers (Cray X-MP, Y-MP, 2). From chemistry-request@ccl.net Fri Oct 18 20:30:37 1991 Date: Fri, 18 Oct 91 17:16:53 PDT From: defrees@almaden.ibm.com To: chemistry@ccl.net Status: R We are looking for a postdoc to work in the Center for Computational Chemsitry (CCC) at IBM Almaden Research Center. One of this postdoc's principal responsibilities will be helping port the upcoming release of Gaussian to VM, MVS, and AIX/370 operating systems, so programming experience is required. In addition, the postdoc will have an opportunity to do research in collaboration with members of CCC. If you know of any candidates, either in your group or elsewhere, please ask them to mail their cv to: Doug DeFrees; IBM Almaden Research Center K84/801; 650 Harry Rd.; San Jose, CA 95120. They could also fax it to (408)927-2100. Thanks, Doug DeFrees