From chemistry-request@ccl.net Thu Aug 22 08:49:46 1991 Date: Thu, 22 Aug 91 08:38:09 EDT From: kpc23%CAS.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU (Kevin P. Cross Ext. 3192 Room 2209B) Subject: Re: Superimposition Software To: "Bob Goldstein 6-6664" Status: R A Fast and Numerically Stable Algorithm for Superimposition of 3D Objects, that is independent of the size of those objects (!), has been written by Manfred J. Sippl and Hans Stegbuchner in Computers and Chemistry Vol 15, No. 1, 1991, 73-78. The C source code is available from M. J. Sippl by writting to 1sippl@edvz.uni-salzburg.ada.at. I have had a chance to exercize this code for the last 6 months and hardily endorse its speed and robustness. Kevin P. Cross Research Chemical Abstracts Service kpc23@cas From chemistry-request@ccl.net Thu Aug 22 10:31:59 1991 Date: Thu, 22 Aug 91 10:13:25 GMT-0500 From: bash@next1.sb.fsu.edu (Paul Bash) To: chemistry@ccl.net Subject: Workshop: High Performance Computing and Grand Challenges in Structural Biology Status: R begin 666 .tar.560.Workshop__High_Perfo_.attach M'YV0:=R0*8/'A1PZ9@`H7,BPH<.'$"-*G$BQ(HB+-F#```'@H@P8,F)PO.B1 MQDB2%V/$L%'CQL4:,&K0N%%#ALT9)%O>D-&QHL^?0(,*'4JTJ-&C2),J7$AAR2=(04'D*(1!!,,+'>$45,`<*%('PG115#4%$% MB4R`($023S#QQ!%9^$==B"`889@<:9`11HQTA$%'&2!4X48:=I0AQU5TY,$" M"#+0T((,+BE151UUY0$"::6!2&1V5(3!!AMAH!'&''-`MJ61AR49AI#7*3`% M'%O-<=@<.H`@)!5H0#D%'7+4,08==EDK8!0E5D@$!' 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I was an "observer" sponsored by the NRC. I was attached to the Working Group on Theoretical Chemistry. As there were only two members of the working group, I wound up doing more than just observing. The working group was just getting started. The discussion was basically "What could the IUPAC do to help theoretical chemistry?" After a couple of hours, I suggested that maybe we should get the opinions of more than 3 people. This list seemed like a good place to start. The IUPAC is, of course, most well known for its work on nomenclature. It also reviews standards, such as publishing volumes on thermodynamic data. They also sponsor some workshops and conferences, and publish Chemistry International. The IUPAC is, however, looking for new areas and ventures, so ideas need not be limited to the traditional areas. Two suggestions, one traditional and one non-traditional, were discussed. One suggestion was a dictionary of acronyms, i.e. MNDO, MSA, etc. The other was an online directory of international anonymous FTP sites for public domain chemical software. These are just samples, but feel free to comment on them. The IUPAC, although international, seems to be more of a European organization, so I would be particularly interested in the comments of the European community. I would also like to mention that I am not a member of IUPAC, so try to keep any flames about the organization from getting personal. I will take any responses I receive and summarize them for Ron Brown in Australia (who is a member), as well as for the list if there is sufficient interest. Please send any comments to me directly. Thanks in advance. Dan Calef CALEF@HEVXA.LLNL.GOV Fax (415)422-2382 From chemistry-request@ccl.net Thu Aug 22 13:26:55 1991 Date: Thu, 22 Aug 1991 13:10:59 EDT From: BIOTERA@SCRI1.SCRI.FSU.EDU (Structural Biology Workshop) Subject: WORKSHOP: Computational Structural Biology **Revised** To: chemistry@ccl.net, BIOTERA-PLANNING@scri.fsu.edu Status: R FIRST ANNOUNCEMENT OF THE WORKSHOP (Ammended notice) HIGH PERFORMANCE COMPUTING AND GRAND CHALLENGES IN STRUCTURAL BIOLOGY Florida State University, 24-27 January 1992 Tallahassee, Florida Sponsors: The Structural Biology Program and the Supercomputer Computations Research Institute (SCRI) at Florida State University. Speakers: Axel T. Brunger (Yale) Ken A. Dill (UCSF) William A. Goddard III (Cal Tech) Robert Langridge (UCSF) Richard A. Friesner (Columbia) Michael Levitt (Stanford) Arnold T. Hagler (Biosym) Herbert Hauptman (Buffalo) Peter A. Kollman (UCSF) Robert L. Jernigan (NIH) James A. McCammon (Houston) Barry Honig (Columbia) Peter A. Kollman (UCSF) Phillip Phillips (MIT) Dennis R. Salahub (Montreal) John D. Joannopoulos (MIT) Harold A. Scheraga (Cornell) William L. Jorgensen (Yale) Klaus Schulten (Illinois) Martin Karplus (Harvard) Arieh Warshel (USC) Peter Wolynes (Illinois) Presentations will be given by the following computer companies that are designing massively parallel computers with Teraflop capabilities : Cray Research Kendall Square Research IBM Thinking Machines Intel Presentations will be given also by the following agencies on their role and policies regarding the new High Performance Computing Initiative: NSF NIH DOE 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. ADDITIONAL INFORMATION: The number of participants is limited to 150-200. The registration fee is $250.00 which will cover: (a) welcoming reception, (b) 3 breakfasts, (c) 3 lunches, and (d) one dinner. The workshop will be held over a weekend so that airfares will be quite reasonable, $350.00 - $500.00 for 21 days advance purchase. The hotel rate is $54 (single or double occupancy) per night. The organizers would like to encourage participation of graduate students and post-doctoral fellows. We hope to be able to provide some financial support to a selected number of individuals of this group. There will be at least one poster session during the workshop. Please indicate below if you would like to give a poster. For additional information, contact: Paul Bash, Department of Chemistry, Florida State University, Tallahassee, Fl. 32306, bash@ibm4.scri.fsu.edu Tel: (904)-644-2492, FAX: (904)-644-8281 or Hagai Meirovitch, Supercomputer Computations Research Institute, Florida State University, Tallahassee, Fl. 32306, hagai@scri1.scri.fsu.edu, Tel: (904)-644-7032, FAX: (904)-644-0098. TO BE INCLUDED ON THE WORKSHOP MAILING LIST: Please e-mail the following information via internet: biotera-planning@scri.fsu.edu NAME: ______________________________________________ POSITION: _____________________________________________ If a student or a post-doc give name of superviser SUPERVISER:______________________________________________ DEPARTMENT:______________________________________________ INSTITUTION: ______________________________________________ ADDRESS: _____________________________________________ _____________________________________________ CITY, ST ZIP: ______________________________________________ RESEARCH INTERESTS:_________________________________________ ____________________________________________________________ ____________________________________________________________ VOICE PHONE: _____________________ FAX PHONE: _____________________ INTERNET E-MAIL ADDRESS: ________________________________________ LIKELIHOOD OF: ATTENDANCE ____% POSTER ____% TITLE OF POSTER:____________________________________________ ______________________________________________________________ NAMES OF OTHER AUTHORS ON THE POSTER: _____________________________________________________________ _____________________________________________________________ From chemistry-request@ccl.net Thu Aug 22 19:42:01 1991 Date: Thu, 22 Aug 91 23:09:48 GMT From: Joe Leonard To: chemistry%ccl.net%apgea.army.mil@crdec7.apgea.army.mil Subject: Pete Petillo contact information Status: R Pete, if you read this bboard (or if somebody who knows Pete reads this bboard) please let me know how to call/email... Apologies if there's one "l"... Joe Leonard Stardent Computer From chemistry-request@ccl.net Thu Aug 22 23:57:12 1991 Date: Thu, 22 Aug 91 23:45:37 EDT From: states@ncbi.nlm.nih.gov (David States) To: chemistry@ccl.net Subject: Re: IUPAC and Theoretical/Computational Chemistry Status: R Dan Calef writes: "What could the IUPAC do to help theoretical chemistry?" Standard data description semantics would be a good to place start. Ideally we would like to be able to pipe the output of one program directly into another program without losing data or accuracy. To exchange data between programs (or databases) it is necessary to agree on both the syntax for the data and a set of semantics. A syntax is just a set of rules for how abstract entities will be transmitted, ie. how do you send a string label X or a floating point value Y. A number of syntax definitions already exist (we are working with ASN.1, an ISO standard, but there are others) so don't reinvent the wheel. The hard part of the problem is agreeing on semantic rules. When I say the energy was x, do I mean calories (gram), calories (kg), kcal/mole, joules, ergs, electron volts ... If units are included, do kcal/mole, Kcal/mole, kcal/Mole, KCAL/MOLE all mean the same thing? How do you describe an electron wavefunction? When a program expects kcals/mole, and it gets ergs, the results are not going to be pretty. The crystallographic community has gone a long way towards a standard semantic in agreeing on CIF (Crystallographic Information Files) for direct submission of manuscripts and data, and they have put alot of work into agreeing on a standard set of dictionaries for describing such data. These dictionaries are really a semantic definition. It would be very nice to have a similar set of rules for working with theoretical data, and IUPAC seems like a good place to do it. David States National Center for Biotechnology Information / National Library of Medicine