From hanger@carbon.chem.csiro.au Tue Sep 1 02:26:31 1992 Date: Tue, 1 Sep 92 16:31:34 EST From: Samantha Hanger Subject: Postdoctoral position in organic chemistry To: chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, SYNTHETIC ORGANIC CHEMIST 3 YEAR POST DOCTORAL FELLOWSHIP AU$36K TO $39K + SUPERANNUATION CSIRO, Division of Chemicals and Polymers, Melbourne, Australia The Division's Fine Chemical Program carries out research aimed at the invention of new chemicals for evaluation as crop protection agents and new chemical processes for use by the Australian chemical industry. A synthetic organic chemist is required to join this Program. You will be expected to be highly skilled in modern methods of organic synthesis and analysis and you will be required to work as a member of a committed team of chemists. We would like to discuss this position with chemists who have experience in the use of microbial and enzymatic methods in synthesis as well as with those skilled in more traditional areas. The Division is well equipped for chemical research, being well supported by analytical, process scale, computational and fermentation facilities. You should possess a PhD degree or equivalent qualification in organic chemistry, and have a proven record of achievement in research. The degree must have been awarded within the last three years. Good written and oral communication skills are also a pre-requisite. Mr Lewis Hewertson can provide further information on this position, telephone (61-3) 542 2479 of fax (61-3) 543 8160. A selection criteria and duties statement are available on request. Please send your application including details of your skills, qualifications and work achievements, quoting Reference 92/5 to the Personnel Officer, CSIRO Division of Chemicals and Polymers, Private Bag 10, Clayton 3168, by 27 November 1992. Electronic mail addresses: Personnel hanger@carbon.chem.csiro.au or Dr. Greg Simpson (greg@carbon.chem.csiro.au) CSIRO IS AN EQUAL OPPORTUNITY EMPLOYER __________________________________________________________________________ Samantha Hanger Voice: 61-3-542-2244 Personnel Officer Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. From omar@malena.crs4.it Tue Sep 1 03:06:07 1992 To: chemistry@ccl.net Subject: Re: motecc summary Date: Tue, 01 Sep 92 09:05:42 +0100 From: Omar G. Stradella Your message dated: Mon, 31 Aug 92 10:43:37 A >Here is the promised summary on MOTECC. > >I was able to contact CRS4, who are distributing the package at the time. >Below are the relevant addresses and e-mail contacts for Dr. Clementi and >CRS4. > >Below the information on CRS4 are some other (possibly outdated) contacts, >which I did not verify. > > Here are some other responses, none of which I verified. Some appear to be > out of date by now. Yes, all the following information is not valid any more. > ---------------------------------------------------------------------------- > MOTECC is available from IBM > > International Business Machines Corporation > Kingston New York 12401 USA > ---------------------------------------------------------------------------- > You obtain it by signing a joint study agreement with IBM and paying something > in the order of US$ 200. > There are two volumes of documentation, edited by Clementi. > Contact your local IBM reps (they probably won't know) and have them contact > their nearest scientific support center (IBM people at Basel are informed). > ---------------------------------------------------------------------------- > Contact address for MOTECC as of 1991: > Dr.Daniel Frye > Scientific and Engineering Computations > Department 48B/428 > Neighborhood Road > Kingston, NY 12401 > ---------------------------------------------------------------------------- > MOTECC -- Modern Techniques in Computational Chemistry is an IBM software > Club which was organized by Enrico Clementi. > You were paying IBM some $500 and got in exchange 20 or something > software packages from atomic ab initio to molecular dynamics. > With the programs you were getting the set of manuals and a very nice book. > > In 1991 the group of Clementi was dissolved. The only person who stayed > in Kingston IBM is Michel Dupuis, michel@kgnvma.vnet.ibm.com. > You may ask him for details. The group of Clementi was not "dissolved" but we moved to our present location in CRS4. -- **************************************************************************** * Dr. Omar G. Stradella - omar@crs4.it * * CRS4 - Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna * * - Centre for Advanced Studies, Research and Development in Sardinia * * -------------------------+----------------------------+----------------- * * Casella Postale 488 | Via Nazario Sauro, 10 | 39 13' 19" North * * 09100 Cagliari CA | 09123 Cagliari CA | 9 6' 17" East * * Italy | Italy | * * -------------------------+----------------------------+----------------- * * Phone: +39 70 27 96 236 FAX: +39 70 27 96 220 * **************************************************************************** From sender@chemdc1.tau.ac.il Tue Sep 1 03:22:25 1992 Date: Tue, 1 Sep 92 10:17:30 -0100 From: sender@chemdc1.tau.ac.il (Senderowitz Hanoch) To: CHEMISTRY@ccl.net Subject: MGS Autumn meeting Hello everybody Does anyone know what's happening with the MGS Autumn meeting on 'Entropy and Solvation' held at Oxford on September 17 and 18? We have been trying to contact Dr. Forster and Dr. Broughton via e-mail, Fax and telephone for the last 3 weeks but got no reply and time is running real short... Thanks, Hanoch Senderowiz (sender@chemdc1.tau.ac.il) From RWOODS@VAX.MOLECULAR-BIOPHYSICS.OXFORD.AC.UK Tue Sep 1 05:05:39 1992 Date: Tue, 1 Sep 92 10:08 GMT From: RWOODS@VAX.MOLECULAR-BIOPHYSICS.OXFORD.AC.UK To: CHEMISTRY Subject: ESP Charge Fluctuations In response to Mark Murcko's question about choosing ESP charge models I would like to mention that while the fluctuations are dependant on the sampling algorithm it is often possible to attenuate the fluctuations by fitting the monopoles to a sub-set of the atoms. In particular, in the case of C-H bonds, especially in methyl groups, we found that fitting the monopoles just to the C atoms gave much more stable values, regardless of conformational changes and sampling variations. This "united atom" approach may be approximated by summing the fitted H-charges into the C atomic charge. The question of sampling method raises an even more complex issue, namely, given a "good" algorithm what is the best approach to handling charge variations that are a function of CONFORMATION? At present, our approach is to use the united atom charges discussed above. While it may not make everyone happy it is much more stable and gives virtually identical results for dipoles and molecule-molecule interaction energies (even H-Bonds provided H's involved in polar bonds such as N-H and O-H are included in the fitting). It may be necessary to include a seperate functional for charges in MM or MD simulations. Something along the lines of Charge(theta)=F(theta) as in torsional potentials, especially for systems whose dipoles change markedly with conformation. I would be very interested in any comments addressing the issue of conformation-dependant charges. Robert J. Woods Glycobiology Institute University of Oxford South Parks Road Oxford, OX1 3QU From JRENE%CCIVS1@FRMOP53.CNUSC.FR Tue Sep 1 08:55:46 1992 Date: Tue, 1 Sep 1992 14:55 EDT From: JRENE%CCIVS1@FRMOP53.CNUSC.FR Subject: IRMA and related relaxation matrix programs To: chemistry@ccl.net >I was going through some old news printouts last night, and came across a >reference to a package called IRMA - relaxation matrix software, by Kaptein in >Holland. >The printout did not have a sender on it, so I was wondering: > > Has anybody heard of it? > Do you know what it does? > Can it be obtained easily, and preferably without money? > Now if my information is correct, IRMA is a thing of the past. It is now part of a software package commercialized by BIOSYM. Of course you might still find the initial versions. The best way to know is to ask Rolf Boelens from the Kaptein group (I don't think that anyone of that group is on this list). His e-mail address is boelens@ruucmr.chem.ruu.nl On the subject of relaxation matrix programs, I found in a number of "Methods in Enzymology" (Vol. 176 part A p. 169) an article where the CORMA program (James and Keepers) was used for relaxation matrix calculations. It was mentioned in the appendix that the program is available from Dr Thomas James Department of Pharmaceutical Science - UCSF CA 94143-0446 San Francisco. (I have no e-mail address for him) Another group that, I think, develops such programs is Sykes' at Edmonton - Canada. jean-rene ALATTIA adresse personnelle INTERNET: jrene%ccivs1@frmop53.cnusc.fr adresse personnelle BITNET : jrene%ccivs1@frmop53.bitnet adresse generale RMN : ccipe@frmop53.cnusc.fr ccipe@frmop53.bitnet From DSMITH@uoft02.utoledo.edu Tue Sep 1 08:59:34 1992 Date: 01 Sep 1992 08:59:18 -0400 (EDT) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: internet notoriety To: chemistry@ccl.net Welcome back to the Chemistry mailing list. As many of you know, I am a frequent and sometimes opinionated poster to this list. Just how much was brought home to me last week at the ACS meeting in Washington, D.C. when many, many people who I have never met walked up to me, saw my name on my badge, and said "Hi, Doug" or "So you're Doug Smith." Luckily, virtually all of those who spoke with me were not unpleasant and did not have an unpleasant attitude towards me. (Maybe those who hate me and my electronic verbosity just didn't bother to stop and talk.) Anyway, it was good meeting all of you - I hope that you can say the same about me. It can be much better having a face to associate with email. Joe and Andy - you were the other two names mentioned most often as most active. (Jan - thank you for the opportunity your mail exploder has provided me to become known outside of the Toledo, OH area.) Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From BPRWAS@ubvms.cc.buffalo.edu Tue Sep 1 09:31:03 1992 Date: 01 Sep 1992 09:30:18 -0400 (EDT) From: BPRWAS@ubvms.cc.buffalo.edu Subject: Re: ESP Charge Fluctuations To: chemistry@ccl.net Organization: University at Buffalo Dear Netters, The dilemma how to obtain "best" charges fitting ESP seems to be an endless problem due to arbitrary choices involved. An alternative approach could be based on the cumulative atomic multipole moments which can be analytically decomposed into sets of off-atom charges (see for example THEOCHEM, 256,91(1992). Point charges of gradually increasing accuracy can be analytically derived from any quantum chemical wavefunction (SCF, CI, MP2, MRD-CI, crystal orbital, etc.) without involving costly calculations of electrostatic potential grid and approximate and arbitrary fitting process. Moreover, due to transferability (limited) of atomic multipole moments between various conformers (after approppiate transformation) point charge models for other conformations can be inexpensively generated from CAMM. It works even for intra-molecular interactions, as we were able to reproduce this way torsional barrier for H-S-S-H ! Andrzej Sokalski BPRWAS@UBVMS (till Sept 16) SOKALSKI@PLWRTU11 (after Sept 16) From carmen@tethys.ph.albany.edu Tue Sep 1 11:49:05 1992 Date: Tue, 01 Sep 1992 11:48:30 EDT From: carmen@tethys.ph.albany.edu To: chemistry@ccl.net Subject: Albany Conference on Computational Biology * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * FINAL CALL FOR PARTICIPANTS * * * * SECOND ALBANY CONFERENCE ON COMPUTATIONAL BIOLOGY * * * * "PATTERNS OF BIOLOGICAL ORGANIZATION" * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * YOUNG INVESTIGATOR AND DISCUSSANT AWARDS * * * * * * * * * * * * * * * * * * * * * * * * * * * GENERAL CONFERENCE DESCRIPTION The Second Albany Conference on Computational Biology will be held October 8-11, 1992 in Rensselaerville near Albany, New York. The aim of this conference (like that of the 1990 Albany Conference) is to explore the computational tools and approaches being developed in diverse fields within biology, with emphasis this year on topics related to organization and self-assembly. The conference will be designed to provide an environment for a frank and informal exchange among scientists and mathematicians that is not normally possible within the constraints of topical, single-discipline meetings. The theme of the Conference, "Patterns of Biological Organization", will be developed in five sessions on topics ranging from the level of sequence to the level of embryo development. Leading specialists in the various disciplines are being invited, with the degree of involvement in novel computational approaches as one of the most important criteria for selection. MEETING AWARDS FOR MATHEMATICIANS AND YOUNG SCIENTISTS We are seeking an interdisciplinary audience: mathematicians and computer scientists as well as biologists. To encourage participation of mathematics and computer science specialists outside the area of biology, we will award waivers of meeting fees ($475 each) to three who are willing to serve as discussants at the meeting. Also, fees will be waived for ten "young investigators" (graduate students, postdocs, junior faculty), to be selected from among the specialties represented at the conference. Individuals seeking either type of award should submit an application (see below) and include a CV and a short letter explaining their interest in attending the meeting. "Young Investigator" awardees will be expected to submit a poster and so applicants should include an abstract with their application. CONFERENCE FORMAT The conference will consist of three morning and two evening sessions over a period of three nights and days (Thursday afternoon through Sunday morning). Each session will be comprised of three or four 30-minute talks interspersed by question-and-answer periods of 15-20 minutes. Afternoons are free for discussion, viewing posters (which all participants are invited to bring), and workshops (some planned, others impromptu). Workshop titles include "structure data bases" and "mechanisms of morphogenesis". In addition, a workshop is planned for Thursday afternoon that will introduce non-biologists to the main issues of macromolecular and cellular structure to be addressed at the meeting. CONFERENCE SESSIONS AND SPEAKERS Keynote Address Thursday PM ---------------------------- Prof. Hermann Haken, Univ. Stuttgart Concepts of Bio-synergetics Session 1 Friday AM Sequence analysis and secondary structure --------------------------------------------------------------- Discussion leader: George Berg State Univ. of New York, Albany 518-442-4267 BERG@CS.ALBANY.EDU Speakers: David L. Waltz, Thinking Machines, Inc. Protein secondary structure prediction using hybrid representation Jean Michel Claverie, NCBI, NIH Gene identification Michael Zuker, National Research Council of Canada Structural analysis by energy dot plot of a large mRNA Stephen Altschul, NCBI, NIH Scoring systems for macromolecular sequence comparison Session 2 Friday PM Macromolecular function --------------------------------------------- Discussion leader: Jacquelyn Fetrow State Univ. of New York, Albany 518-442-4389 JACQUE@ISADORA.ALBANY.EDU Speakers: Judith Hempel, Biosym Technologies, Inc. Conformational analysis of peptides and protein loop regions Fred E. Cohen, UCSF Pharmaceutical design from protein structure Chris Lee, Stanford University Steric fit in protein stability and substrate specificity Francois Michel, Centre de Genetique Moleculaire, CNRS (France) Three-dimensional architecture of a catalytic RNA, as revealed by comparative sequence analysis Session 3 Saturday AM Development ----------------------------------- Discussion leader: John Reinitz Yale Univ., New Haven, CT 203-785-7049 REINITZ-JOHN@CS.YALE.EDU Speakers: Michael Levine, UC-San Diego The transcriptional control of stripes in the Drosophila embryo John Reinitz, Yale University Circuitry from gene expression George Oster, UC-Berkeley Brownian machines Stuart A. Newman, New York Medical College Generic physical mechanisms as templates for development and evolution. Session 4 Saturday PM Recognition and assembly ------------------------------------------------ Discussion leader: Joachim Frank Wadsworth Center and State Univ. of New York, Albany 518-474-7002 JOACHIM@TETHYS.PH.ALBANY.EDU Speakers: David DeRosier, Brandeis University Structure and assembly of the bacterial flagellum: protein folding linked to flagellin polymerization Phoebe L. Stewart, The Wistar Institute Bridging the resolution gap between x-ray crystallography and electron microscopy John Sedat, UCSF Visualization and analysis of multidimensional cellular structures Session 5 Sunday AM Tertiary structure prediction --------------------------------------------------- Discussion leader: Charles Lawrence Wadsworth Center, and State Univ. of New York, Albany 518-473-3382 CEL@BIOMETRICS.PH.ALBANY.EDU Speakers: Rick Fine, Biosym Technologies, Inc. Towards reliable modeling of antibody combining sites: insights from canonical structures, conformational search, and solvation analysis Stephen Bryant, NCBI, NIH A residue contact potential for threading sequence through folding motif James U. Bowie, UCLA Assessing the compatibility of a protein sequence with a three-dimensional structure CONFERENCE SITE The conference, one of the Albany Conference series held annually since 1984, will take place at the Rensselaerville Conference Center, located 30 miles southwest of Albany, NY in the Helderberg Mountains. The Institute offers on-campus facilities including a large auditorium with audio-visual equipment and smaller conference halls for informal workshops and poster sessions. The Weathervane Restaurant, located on-campus and formerly the carriage house of the Huyck estate, provides meals and refreshments, while overnight lodging is available in the modern & classic estate houses. Rooms are assigned in advance to registrants, and transportation to and from Rensselaerville is provided from the airport, train and bus stations. The rural, secluded setting of the conference, the limited number of participants and the scheduling of sessions in the morning and the evening -- leaving the afternoons free -- are intended to facilitate informal discussions among conference participants. REGISTRATION INFORMATION CONFERENCE FEE: $475 includes registration, accomodations (double occ.), meals and transportation between the conference center and Albany airport. Payment of the full fee will be required by SEPT. 31, 1992. Please note that neither the Albany Conferences nor the Rensselaerville Conference Center accepts credit cards. APPLICATION DEADLINE: SEPTEMBER 10, 1992 For further registration information contact: Conference coordinator, Carole Keith, 518-442-4327, FAX 518-442-4767, carole@uacsc2.albany.edu - or send your application & abstract (unfolded) to The Albany Conference, P.O. Box 8836, Albany, NY 12208-0836. MEETING AWARDS Graduate students, postdocs, and junior faculty who would like to be considered for a Young Investigator award should submit with the registration form - a CV, a brief letter explaining research interests and a poster abstract. Graduate students should also include a letter of recommendation from a faculty advisor. Mathematicians and computer scientists who would like to apply for a Discussant award should include a CV and a brief statement explaining how their expertise relates to the theme of the meeting. Applications from members of groups that are underrepresented in this field (women and racial minorities) are strongly encouraged. - - - - - - - - - - - - - - - - - - - - - - - - You may use the following "E-Mail application form" to register: Name: Organization: Business Address: City: State: Zip: Business Phone: Fax: If you plan to submit a poster, please include its title and (if ready) a short abstract. (You will be asked to provide by Sept. 16 a one-page, camera-ready version of the poster abstract, using 1.5 inch borders, for the meeting workbook.) Indicate if you wish to be considered for a Young Scientist or Discussant Award. From zheng@violet.berkeley.edu Tue Sep 1 12:29:29 1992 Date: Tue, 1 Sep 92 09:29:19 -0700 From: zheng@violet.berkeley.edu To: chemistry@ccl.net Subject: van der Waals' radii Here are some references: Pauling (1940) The nature of chemical bond (2nd edition), Cornell University Press. Bondi (1964) J. Phys. Chem. 68, 441-51. Rosenfield et al (1977) JACS 99, 4860-2. Britton and Dunitz (1980) Helv. Chim. Acta 63, 1068-73. Nyburg and Faerman (1985) Acta Cryst. B41, 1274-9. Nyburg et al (1987) Acta Crsyt. B43, 106-10. Also, Accurate Molecular Structures: Their determination & importance, 1992. The call number is: QD461 A33 1992. Hope this is useful. Yajun Zheng