From BIOSCI-REQUEST Wed Jun 7 07:50:27 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id HAA03291 for rna-list; Wed, 7 Jun 1995 07:50:27 -0700 Received: from po2.andrew.cmu.edu (PO2.ANDREW.CMU.EDU [128.2.10.102]) by net.bio.net (8.6.11/8.6.6) with ESMTP id HAA03287 for ; Wed, 7 Jun 1995 07:50:22 -0700 Received: (from postman@localhost) by po2.andrew.cmu.edu (8.6.12/8.6.12) id KAA07479; Wed, 7 Jun 1995 10:50:09 -0400 Received: via switchmail; Wed, 7 Jun 1995 10:50:08 -0400 (EDT) Received: from unix14.andrew.cmu.edu via qmail ID ; Wed, 7 Jun 1995 10:49:41 -0400 (EDT) Received: from unix14.andrew.cmu.edu via qmail ID ; Wed, 7 Jun 1995 10:49:39 -0400 (EDT) Received: from mms.4.60.Jan.26.1995.18.43.47.sun4c.411.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix14.andrew.cmu.edu.sun4c.411 via MS.5.6.unix14.andrew.cmu.edu.sun4c_411; Wed, 7 Jun 1995 10:49:38 -0400 (EDT) Message-ID: <4jpPm2W00YUqI6gbJ_@andrew.cmu.edu> Date: Wed, 7 Jun 1995 10:49:38 -0400 (EDT) From: Michael Tor Klawansky To: Outbound News Subject: CCL:METHODS OF MOLECULAR MECHANICS WORKSHOP Cc: Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , rna@net.bio.net, chemistry@osc.edu ***** NOTE:When replying please reply to ropelews@slave.psc.edu ***** "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. TRAVEL, MEALS AND HOTEL ACCOMMODATIONS FOR RESEARCHERS AFFILIATED WITH U.S. ACADEMIC INSTITUTIONS ARE SUPPORTED BY THIS GRANT. Enrollment is limited to 20. An application form is included. Deadline for applications is: June 22, 1995. Please direct inquires or send the following application form to blankens@psc.edu. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by June 22, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From BIOSCI-REQUEST Fri Jun 16 14:14:14 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id OAA01053 for rna-list; Fri, 16 Jun 1995 14:14:14 -0700 Received: from regulus.lifesci.ucla.edu (regulus.lifesci.ucla.edu [128.97.8.87]) by net.bio.net (8.6.12/8.6.6) with SMTP id OAA01031; Fri, 16 Jun 1995 14:14:02 -0700 Received: by regulus.lifesci.ucla.edu (Sendmail 5.67b/1.00-lifesci) id AA03313; Fri, 16 Jun 1995 14:13:32 -0700 Received: from smtpgate.lifesci.ucla.edu(128.97.8.227) by regulus.lifesci.ucla.edu via smap (V1.3) id sma003292; Fri Jun 16 14:13:13 1995 Received: by smtpgate.lifesci.ucla.edu with Microsoft Mail id <2FE1F450@smtpgate.lifesci.ucla.edu>; Fri, 16 Jun 95 14:14:56 PDT From: "Zeiler, Brian M'bio" To: methods-and-reagents , RNA Subject: 3-D RNA modeling Date: Fri, 16 Jun 95 14:13:00 PDT Message-Id: <2FE1F450@smtpgate.lifesci.ucla.edu> Encoding: 13 TEXT X-Mailer: Microsoft Mail V3.0 Hello fellow netters, I am conducting some experiments relating to RNA structure. I work with small RNAs, usually less than 100 nucleotides. I have access to a good folding program, mulfold, through the GCG package and have extensively folded my molecules and got nice two dimensional representations. However, it is becoming clear that I should be concerned with the three dimensional structure of my molecules. Does anyone know if three dimensional modelling programs exist? Any help and insights will be welcome. Brian Zeiler brianz@microbio.lifesci.ucla.edu From BIOSCI-REQUEST Mon Jun 26 06:59:55 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id GAA00953 for rna-list; Mon, 26 Jun 1995 06:59:55 -0700 Received: from vax8.cfsan.fda.gov (vax8.CFSAN.FDA.GOV [150.148.80.20]) by net.bio.net (8.6.12/8.6.6) with ESMTP id GAA00950 for ; Mon, 26 Jun 1995 06:59:53 -0700 From: SMG@vax8.cfsan.fda.gov Received: from VAX8.CFSAN.FDA.GOV by VAX8.CFSAN.FDA.GOV (PMDF V4.3-12 #8689) id <01HS5OAOH2HS0000XH@VAX8.CFSAN.FDA.GOV>; Mon, 26 Jun 1995 09:54:48 -0400 (EDT) Date: Mon, 26 Jun 1995 09:54:48 -0400 (EDT) Subject: Ribosomal Operons To: rna@net.bio.net Message-id: <01HS5OAOH3G20000XH@VAX8.CFSAN.FDA.GOV> X-VMS-To: IN%"rna@net.bio.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT I am interested in the use of ribosomal sequences for constructing probes and primers used in molecular diagnostics and subtyping in food microbiology. This work has raised several questions regarding the occurance of multiple ribosomal operons in microbial genomes, and I am hoping that the members of this list can point me to the answers. First, is there a list of the number of ribosomal operons that occur in different microbial genomes for a range of species. I have seen papers that refer to the number for several individual species (E. coli, B. subtilis, etc.), but not a general listing, or general review for that matter. Second, what is known about sequence conservation between the different operons that occur in a single genome? Do the ribosomal coding sequences differ? How much variability is there in the spacer regions? Are the answers to these questions consistent in different species? Third, while I think of it, what is the easiest way to count how may operons there are in the genome of a species or strain? Fourth, is anything known about the relative transcription rates for different operons in the same genome? Thanks for your help. Steven Gendel Chief, Biotechnology Studies Branch FDA, Center for Food Safety and Applied Nutrition 6502 S. Archer Summit, Illinois 60501 708-728-4110 smg@vax8.cfsan.fda.gov