From BIOSCI-REQUEST Sat Apr 1 14:21:42 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id OAA22853 for rna-list; Sat, 1 Apr 1995 14:21:42 -0800 Received: from selway.umt.edu (selway.umt.edu [150.131.14.2]) by net.bio.net (8.6.11/8.6.6) with SMTP id OAA22850 for ; Sat, 1 Apr 1995 14:21:39 -0800 Received: by selway.umt.edu (5.65/DEC-Ultrix/4.3) id AA26182; Sat, 1 Apr 1995 15:21:35 -0700 Message-Id: <9504012221.AA26182@selway.umt.edu> Subject: transcription problem To: rna@net.bio.net (rna) Date: Sat, 1 Apr 1995 15:21:35 -0700 (MST) From: "Douglas J Bucklin" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Content-Length: 1032 Netters: We are trying to synthesize several RNAs. For most we have no problem, but two of them are giving us problems. The two troublesome ones break down into one that works O.K., and another that is quite similar, but will not appear. We transcribe off of oligo templates with T7 RNA Pol. and use the protocol of Milligan(sp?) et al. (NAR, late 80's) for the reactions. Both RNAs are designed to be stem and loop structures. The sequences are virtually identicle, the one that works does have five extra nucleotides at the 3' end that are not involved in the stem loop. All of the other bases, for both RNAs, are in the stem loop. The first three nucleotides incorporated are G. We have tried templates that are ds only in the promoter region, and fully ds templates. Do any of you have any ideas why two nearly identicle templates would give these results? Do you have suggestions to provide that may aid in getting the troublesome template to produce? Thank you Douglas Bucklin bucklin@selway.umt.edu From BIOSCI-REQUEST Sat Apr 1 17:18:20 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id RAA00513 for rna-list; Sat, 1 Apr 1995 17:18:20 -0800 Received: from selway.umt.edu (selway.umt.edu [150.131.14.2]) by net.bio.net (8.6.11/8.6.6) with SMTP id RAA00506 for ; Sat, 1 Apr 1995 17:18:12 -0800 Received: by selway.umt.edu (5.65/DEC-Ultrix/4.3) id AA18543; Sat, 1 Apr 1995 18:18:06 -0700 Message-Id: <9504020118.AA18543@selway.umt.edu> Subject: transcription II To: rna@net.bio.net (rna) Date: Sat, 1 Apr 1995 18:18:06 -0700 (MST) From: "Douglas J Bucklin" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Content-Length: 802 Netters: I have a second question regarding trascription. After carrying out large scale transcriptions, with the goal of getting approx. 20 nmoles of transcript, what is a good method of purification. Currently we are using gel purification on 3mm polyacryl., 7M urea, TBE gels or biospin exclusion columns. I really don't like any of the methods I have found. They are usually labor intensive. Is there something out there that is quick and reliable. When doing the transcriptions there is often a heavy amount of insoluble goo that is produced. We have found that the RNA is in that fraction. Is that a common experience? How do you redissolve that fraction? Even after heating and diluting the scum still likes to persist. Thank you Douglas Bucklin bucklin@selway.umt.edu From BIOSCI-REQUEST Sun Apr 2 07:31:05 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id HAA02623 for rna-list; Sun, 2 Apr 1995 07:31:05 -0700 Received: from neutron.chem.yale.edu (neutron.chem.yale.edu [130.132.25.75]) by net.bio.net (8.6.11/8.6.6) with ESMTP id HAA02620 for ; Sun, 2 Apr 1995 07:31:03 -0700 Received: by neutron.chem.yale.edu (950215.SGI.8.6.10/940406.SGI.AUTO) for rna@net.bio.net id KAA26473; Sun, 2 Apr 1995 10:30:59 -0400 From: dcs@neutron.chem.yale.edu (Dave Schweisguth) Message-Id: <199504021430.KAA26473@neutron.chem.yale.edu> Subject: Re: transcription II To: rna@net.bio.net (RNA mailing list) Date: Sun, 2 Apr 1995 10:30:58 -0400 (EDT) In-Reply-To: <9504020118.AA18543@selway.umt.edu> from "Douglas J Bucklin" at Apr 1, 95 06:18:06 pm Organization: Dept. of Chemistry, Yale University X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1537 Doug, > I have a second question regarding trascription. After carrying out > large scale transcriptions, with the goal of getting approx. 20 nmoles of > transcript, what is a good method of purification. Currently we are using > gel purification on 3mm polyacryl., 7M urea, TBE gels or biospin exclusion > columns. I really don't like any of the methods I have found. They are > usually labor intensive. Is there something out there that is quick and > reliable. Our lab (which does several-micromole-scale preps for NMR) mostly uses polyacrylamide. Some of us (including me) use HPLC, which is lovely when it works but requires occasional lengthy periods of tinkering. Our usual column is a DEAE 60-7 from Nucleogen (via Rainin). > When doing the transcriptions there is often a heavy amount of > insoluble goo that is produced. We have found that the RNA is in that > fraction. Is that a common experience? How do you redissolve that > fraction? Even after heating and diluting the scum still likes to persist. That's magnesium pyrophosphate. Redissolve it with EDTA (we use 1/10 vol. 0.5 M EDTA) and desalt to taste. Some just spin the ppt out, but as you say that may take some RNA with it. Cheers, -- | Dave Schweisguth For purposes of complying with | | dcs@proton.chem.yale.edu (MIME OK) the New Jersey Right to Know Act: | | http://proton.chem.yale.edu/~dcs/ Contents partially unknown. | | Yale Depts. of MB&B & Chemistry Phone: 203-432-5208 Fax: 203-432-6144 | From BIOSCI-REQUEST Mon Apr 3 02:42:56 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id CAA25605 for rna-list; Mon, 3 Apr 1995 02:42:56 -0700 Received: from ppsw3.cam.ac.uk (pp@mauve.csi.cam.ac.uk [131.111.8.38]) by net.bio.net (8.6.11/8.6.6) with ESMTP id CAA25601 for ; Mon, 3 Apr 1995 02:42:48 -0700 Received: from mole.bio.cam.ac.uk by mauve.csi.cam.ac.uk with SMTP-CAM (PP-7.1) as ppsw.cam.ac.uk; Mon, 3 Apr 1995 09:40:19 +0000 Received: from er1mac04.vrl.path.cam.ac.uk by mole.bio.cam.ac.uk (931110.SGI/MDTG-V1.3@mole.bio.cam.ac.uk) id AA18552; Mon, 3 Apr 95 10:44:33 +0100 Date: Mon, 3 Apr 95 10:44:33 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: Douglas J Bucklin From: etd@mole.bio.cam.ac.uk (Edwin ten Dam) Subject: Re: transcription problem Cc: rna@net.bio.net (rna) Thus spoke the keyboard of Douglas J Bucklin (01*04*95): * Netters: * * We are trying to synthesize several RNAs. For most we have no problem, * but two of them are giving us problems. * The two troublesome ones break down into one that works O.K., * and another that is quite similar, but will not appear. We transcribe * off of oligo templates with T7 RNA Pol. and use the protocol of * Milligan(sp?) et al. (NAR, late 80's) for the reactions. Both RNAs are * designed to be stem and loop structures. The sequences are virtually * identicle, the one that works does have five extra nucleotides at the * 3' end that are not involved in the stem loop. All of the other bases, * for both RNAs, are in the stem loop. The first three nucleotides * incorporated are G. * We have tried templates that are ds only in the promoter region, * and fully ds templates. * Do any of you have any ideas why two nearly identicle templates * would give these results? Do you have suggestions to provide that may * aid in getting the troublesome template to produce? I vaguely remember an article (Milligan et al. (NAR, late 80's as well) where the authors analyse the relative efficiency of templates and found that U's in the first 8 nt's were counterproductive (they led to abortive transcripts). Sorry, can't be more specific at the moment. Good luck, Edwin Edwin ten Dam etd@mole.bio.cam.ac.uk Division of Virology - University of Cambridge Tennis Court Road, Cambridge CB2 1QP, U.K. Phone: +44 1223 336918 - Fax: +44 1223 336926 From BIOSCI-REQUEST Mon Apr 3 15:38:53 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id PAA12853 for rna-list; Mon, 3 Apr 1995 15:38:53 -0700 Received: from LCBVAX.CCHEM.BERKELEY.EDU (lcbvax.cchem.berkeley.edu [128.32.144.208]) by net.bio.net (8.6.11/8.6.6) with SMTP id PAA12847 for ; Mon, 3 Apr 1995 15:38:48 -0700 Message-Id: <199504032238.PAA12847@net.bio.net> Received: from [128.32.144.196] by 128.32.144.196 with SMTP; Mon, 3 Apr 1995 15:38:38 -0700 (PDT) Date: Mon, 3 Apr 1995 14:40:33 -0500 To: bucklin@selway.umt.edu From: jacek@lcbvax.cchem.berkeley.edu (Jacek Nowakowski) Subject: Problems with transcription Cc: rna@net.bio.net On 4/1/95 Douglas Bucklin wrote: > When doing the transcriptions there is often a heavy amount of > insoluble goo that is produced. We have found that the RNA is in that > fraction. Is that a common experience? How do you redissolve that > fraction? Even after heating and diluting the scum still likes to persist. Dave Schweisguth replied on 4/2/95: >That's magnesium pyrophosphate. Redissolve it with EDTA (we use 1/10 vol. >0.5 M EDTA) and desalt to taste. Some just spin the ppt out, but as you say >that may take some RNA with it. To prevent accumulation of the pyrophosphate during the transcription reaction you may also add a small amount ( 1-4units/ml of transcription) of yeast Inorganic Pyrophosphatase (ref. BioTechniques Vol. 9, No. 6 (1990) p.713) It doesn't hurt anything, and it actually improves the yield of transcription. Definitely work up your reaction with EDTA (see above). Jacek Nowakowski (Tinoco lab) From BIOSCI-REQUEST Mon Apr 3 17:38:59 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id RAA20153 for rna-list; Mon, 3 Apr 1995 17:38:59 -0700 Received: from proton.chem.yale.edu (proton.chem.yale.edu [130.132.25.95]) by net.bio.net (8.6.11/8.6.6) with ESMTP id RAA20150 for ; Mon, 3 Apr 1995 17:38:57 -0700 Received: by proton.chem.yale.edu (950215.SGI.8.6.10/940406.SGI.AUTO) for rna@net.bio.net id UAA04580; Mon, 3 Apr 1995 20:38:53 -0400 From: dcs@proton.chem.yale.edu (Dave Schweisguth) Message-Id: <199504040038.UAA04580@proton.chem.yale.edu> Subject: Re: transcription II To: rna@net.bio.net (RNA mailing list) Date: Mon, 3 Apr 1995 20:38:53 -0400 (EDT) In-Reply-To: <9504040005.AA07181@selway.umt.edu> from "Douglas J Bucklin" at Apr 3, 95 06:05:13 pm Organization: Dept. of Chemistry, Yale University X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1093 Douglas Bucklin quoth: > I have played around with HPLC, but our coumn which was found > with the ancient artifacts of King Tut may have been a problem. After > experimenting with the gradient for quite a long time I found a nice > step gradient with NaCl that seemed to separate several peaks nicely. > The peak that corresponded to my gel purified standard was well > isolated. When I looked at the peak contents on a gel I still saw > abortive fragments. The question: What gradient system worked? I use the DEAE column part of "A rapid method for purification of synthetic oligoribonucleotides", BioTechniques 11(5):658-661, 1991. Briefly, that's 20 mM NaOAc, 6 M urea, 20% CH3CN, ph 6.5, 0-1.5M KCl over 50 minutes. Quite reliable, if your HPLC is. Cheers, -- | Dave Schweisguth For purposes of complying with | | dcs@proton.chem.yale.edu (MIME OK) the New Jersey Right to Know Act: | | http://proton.chem.yale.edu/~dcs/ Contents partially unknown. | | Yale Depts. of MB&B & Chemistry Phone: 203-432-5208 Fax: 203-432-6144 | From BIOSCI-REQUEST Tue Apr 18 07:57:53 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id HAA15318 for rna-list; Tue, 18 Apr 1995 07:57:53 -0700 Received: from Eros.EMBL-Heidelberg.DE (eros.EMBL-Heidelberg.DE [192.54.41.21]) by net.bio.net (8.6.11/8.6.6) with ESMTP id HAA15309 for ; Tue, 18 Apr 1995 07:57:20 -0700 Received: from EMBL-Heidelberg.DE by EMBL-Heidelberg.DE (PMDF V4.3-7 #2491) id <01HPHPCUU2XQ48BVB9@EMBL-Heidelberg.DE>; Tue, 18 Apr 1995 16:55:07 +0100 Date: Tue, 18 Apr 1995 16:55:07 +0100 From: Bertrand Seraphin Subject: Job To: RNA@net.bio.net Message-id: <01HPHPCUU2XC48BVB9@EMBL-Heidelberg.DE> X-FAX-defaults: /STN=+49 6221 387 0/SFN=+49 6221 387 306 X-VMS-To: IN%"RNA@net.bio.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=ISO-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE Funded research post-doctoral position available immediately=20 in the laboratory of B. Seraphin in the Gene Expression=20 Programme at EMBL Heidelberg, Germany to study RNA splicing=20 and processing in yeast as well as small nuclear=20 RiboNucleoProtein (snRNP) synthesis in yeast and mammalian=20 systems. Studies are focused on (but not limited to): a) splice site selection and splicing catalysis; b) intron recognition by the splicing machinery; c) protein-RNA interactions and spliceosomal snRNP assembly,=20 particularly function of the Sm proteins; d) structure-function of the RNase P and MRP=20 RiboNucleoProteins. Recent publications include: Seraphin, B. and S. Kandels-Lewis, 3=AB splice site=20 recognition in S. cerevisiae does not require base pairing=20 with U1 snRNA (1993). Cell, 73, 803-812; Kandels-Lewis, S.=20 and B. Seraphin (1993), Role of U6 snRNA in 5' splice site=20 selection. Science, 262, 2035-2039; Lygerou, Z., et al.=20 (1994), The POP1 gene encodes a protein component common to=20 the RNase MRP and RNase P ribonucleoproteins. Genes & Dev.,=20 8, 1423-1433; Seraphin, B (1995). Sm and Sm-like proteins=20 belong to a large family: identification of proteins of the=20 U6 as well as the U1, U2, U4 and U5 snRNPs. EMBO J. in=20 press. Additional projects in the eight other labs of the Gene=20 Expression Programme are targeted to the analysis of RNA=20 processing, transport and translation as well as=20 transcription. EMBL provides an exceptional scientific=20 environment with excellent facilities. This position is funded for 12 month with possibilities of=20 extension. Interested candidates with general background in=20 molecular biology should send a C.V. to B. Seraphin by E- mail (Seraphin@EMBL-Heidelberg.DE) or by mail to B.=20 Seraphin, EMBL, Meyerhofstrasse1, D-69117 Heidelberg,=20 Germany. From BIOSCI-REQUEST Tue Apr 18 12:15:03 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id MAA29077 for rna-list; Tue, 18 Apr 1995 12:15:03 -0700 Received: from andrew.cmu.edu (ANDREW.CMU.EDU [128.2.10.101]) by net.bio.net (8.6.11/8.6.6) with ESMTP id MAA29069 for ; Tue, 18 Apr 1995 12:14:56 -0700 Received: (from postman@localhost) by andrew.cmu.edu (8.6.12/8.6.9) id PAA12909; Tue, 18 Apr 1995 15:14:49 -0400 Received: via switchmail; Tue, 18 Apr 1995 15:14:48 -0400 (EDT) Received: from unix6.andrew.cmu.edu via qmail ID ; Tue, 18 Apr 1995 15:13:49 -0400 (EDT) Received: from unix6.andrew.cmu.edu via qmail ID ; Tue, 18 Apr 1995 15:13:35 -0400 (EDT) Received: from mms.4.60.Jan.26.1995.18.44.27.pmax.ul4.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix6.andrew.cmu.edu.pmax.ul4 via MS.5.6.unix6.andrew.cmu.edu.pmax_ul4; Tue, 18 Apr 1995 15:13:34 -0400 (EDT) Message-ID: <0jZ0xSS00WB7FWtlVg@andrew.cmu.edu> Date: Tue, 18 Apr 1995 15:13:34 -0400 (EDT) From: "Alexander J. Ropelewski" To: Outbound News Subject: CCL:Sequence Analysis Workshop Cc: Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , chemistry@osc.edu, rna@net.bio.net, Outbound News NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS Pittsburgh, Pennsylvania June 4-9, 1995 Pittsburgh Supercomputing Center (PSC) is again offering a five-day workshop on "Nucleic Acid and Protein Sequence Analysis," June 4-9, 1995. It is funded by a grant from the National Center for Human Genome Research of the National Institutes of Health. The workshop will familiarize biomedical researchers in applying supercomputing resources to problems of concern in macromolecular sequence analysis. Emphasis will be on alignment of and pattern extraction from multiple sequences. Participants will gain practical experience on PSC's Cray C-90 and T3D in (1) comparing and aligning sequences, (2) identifying informative patterns in a set of sequences; and (3) using extracted informative patterns to identify related sequences. Researchers will also learn several approaches to database searching and multiple sequence alignment, how to use profile analysis effectively, and how to identify patterns in their sequences. Participants are encouraged to bring sequence analysis problems from their current research. Extensive documentation will be given at the outset on the PSC computing environment as well as on the specific programs to be employed in the workshop. No prior supercomputing experience is required. Workshop leaders are Dr. Gary Churchill, Cornell University, Dr. Michael Gribskov, San Diego Supercomputing Center, and Dr. Hugh Nicholas, PSC. A limited number of grants to cover travel and hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE, IN ADVANCE, UPON ACCEPTANCE INTO THE WORKSHOP. DEADLINE FOR SUBMITTING APPLICATIONS IS FRIDAY, APRIL 21, 1995. Enrollment is lmited to 20 participants. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * PITTSBURGH SUPERCOMPUTING CENTER NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS June 4-9, 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) In order to attend the workshop, will you need funds for travel?___ lodging?___ 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, the sequence analysis problems encountered in your 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. If you have requested travel funds, please include the cost of roundtrip air fare from your home to Pittsburgh and indicate the amount of travel funds you will need. ALL PARTICIPANTS WILL BE REQUIRED TO PAY A $135 ADVANCE REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Please return all application materials by APRIL 21, 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 Wed Apr 19 13:50:20 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id NAA14758 for rna-list; Wed, 19 Apr 1995 13:50:20 -0700 Received: from po7.andrew.cmu.edu (PO7.ANDREW.CMU.EDU [128.2.10.107]) by net.bio.net (8.6.11/8.6.6) with ESMTP id NAA14755 for ; Wed, 19 Apr 1995 13:50:17 -0700 Received: (from postman@localhost) by po7.andrew.cmu.edu (8.6.12/8.6.9) id QAA15612; Wed, 19 Apr 1995 16:50:10 -0400 Received: via switchmail; Wed, 19 Apr 1995 16:50:09 -0400 (EDT) Received: from unix7.andrew.cmu.edu via qmail ID ; Wed, 19 Apr 1995 16:49:26 -0400 (EDT) Received: from unix7.andrew.cmu.edu via qmail ID ; Wed, 19 Apr 1995 16:49:09 -0400 (EDT) Received: from mms.4.60.Jan.26.1995.18.44.27.pmax.ul4.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix7.andrew.cmu.edu.pmax.ul4 via MS.5.6.unix7.andrew.cmu.edu.pmax_ul4; Wed, 19 Apr 1995 16:49:08 -0400 (EDT) Message-ID: Date: Wed, 19 Apr 1995 16:49:08 -0400 (EDT) From: "Alexander J. Ropelewski" To: Outbound News Subject: CCL:Methods of Molecular Mechanics and Dynamics of Biopolymers workshop Cc: Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , rna@net.bio.net, chemistry@osc.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 Wed Apr 19 13:55:07 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id NAA15070 for rna-list; Wed, 19 Apr 1995 13:55:07 -0700 Received: from andrew.cmu.edu (ANDREW.CMU.EDU [128.2.10.101]) by net.bio.net (8.6.11/8.6.6) with ESMTP id NAA15035; Wed, 19 Apr 1995 13:54:53 -0700 Received: (from postman@localhost) by andrew.cmu.edu (8.6.12/8.6.9) id QAA21995; Wed, 19 Apr 1995 16:54:44 -0400 Received: via switchmail; Wed, 19 Apr 1995 16:54:43 -0400 (EDT) Received: from unix7.andrew.cmu.edu via qmail ID ; Wed, 19 Apr 1995 16:52:47 -0400 (EDT) Received: from unix7.andrew.cmu.edu via qmail ID ; Wed, 19 Apr 1995 16:52:36 -0400 (EDT) Received: from mms.4.60.Jan.26.1995.18.44.27.pmax.ul4.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix7.andrew.cmu.edu.pmax.ul4 via MS.5.6.unix7.andrew.cmu.edu.pmax_ul4; Wed, 19 Apr 1995 16:52:36 -0400 (EDT) Message-ID: <8jZLUIi00WB88DHVkO@andrew.cmu.edu> Date: Wed, 19 Apr 1995 16:52:36 -0400 (EDT) From: "Alexander J. Ropelewski" To: Outbound News Subject: CCL:STRUCTURE DETERMINATION FROM NMR Cc: Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , rna@net.bio.net, chemistry@osc.edu, Outbound News , str-nmr@net.bio.net, bruker-users-mail@bloch.cchem.berkeley.edu, ammrl-request@bloch.cchem.berkeley.edu STRUCTURE DETERMINATION FROM NMR Pittsburgh Supercomputing Center June 25-28, 1995 Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a "Structure Determination From NMR" Workshop. The objective is to introduce participants to the different techniques for the elucidation of solution structures of biological macromolecules from nuclear magnetic resonance data. The workshop is free to academic participants. The worskhop will consist of lectures and extensive hands-on sessions. The programs AMBER, Mardigras and MidasPlus will be discussed. 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. Workshop leaders are: Dr. David Case, The Scripps Research Institute; and Drs Thomas James, Julie Newdoll and Uli Schmitz, University of California, San Francisco. 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 April 28, 1995. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * * * * * * PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE STRUCTURE DETERMINATION FROM NMR June 25-28, 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 APRIL 28, 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 Wed Apr 19 23:54:19 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id XAA19419 for rna-list; Wed, 19 Apr 1995 23:54:19 -0700 Received: from degas.imb-jena.de (degas.imb-jena.de [192.124.248.26]) by net.bio.net (8.6.11/8.6.6) with ESMTP id XAA19396 for ; Wed, 19 Apr 1995 23:53:49 -0700 Received: by degas.imb-jena.de (950221.405.SGI.8.6.10/920502.SGI) for rna@net.bio.net id JAA02770; Thu, 20 Apr 1995 09:00:07 +0200 Date: Thu, 20 Apr 1995 09:00:07 +0200 From: jsuehnel@imb-jena.de (Juergen Suehnel) Message-Id: <199504200700.JAA02770@degas.imb-jena.de> To: rna@net.bio.net Subject: RNA on the World-Wide Web RNA on the World-Wide Web ######################### I would like to inform the RNA community that we have recently set up two RNA related world-wide web (www) resources. ============================================================== The first one (The RNA World) is a home page which tries to collect all RNA related www links. Currently, it contains the following entries: The RNA World ------------------------------------------------------------------- Image Library of Biological Macromolecules (IMB Jena) (with images of all RNA structures from the Protein Data Bank and Nucleic Acid Database) Protein Data Bank (Brookhaven) (including RNA structures)[Gopher Link] Protein Data Bank (Brookhaven) (including RNA structures)[WWW Link] The Nucleic Acid Database (Rutgers) RNA Secondary Structures (Boulder, CO) BERLIN - RNA Databank of 5S rRNA and 5S rRNA Gene Sequences (CAOS/CAMM, The Netherlands) rRNA - Database of Ribosomal Subunit Sequences (University of Antwerp, Belgium) Ribosomal Database Project (Urbana, IL) The Ribonuclease P Database (Indiana University, North Carolina State University) Introduction Archive Compilation of tRNA and tRNA Gene Sequences (EMBL) Small RNA Compilation (EMBL) (1991 !!!) RNA Folding Software Guide (University of California, Irvine) -------------------------------------------------------------------- Its address is: http://www.imb-jena.de/RNA.html . If somebody knows of more RNA resources accessible via the world-wide web I would be grateful to get informed. =================================================================== The second resource is the IMAGE LIBRARY OF BIOLOGICAL MACROMOLECULES (http://www.imb-jena.de/IMAGE.html). Currently, it contains images of all RNA structures available in the Protein Data Bank or the Nucleic Acid Database (about 60 structures), of about 120 proteins and 60 DNA structures. Each structure is described in a short annotation file with bibliographic and sequence information. The image files include a color coded distance plot and various structure images (almost all of them also in stereo). Currently, the total number of RNA image files is about 550 (for the complete LIBRARY 2200). Contrary, to the images provided by the Protein Data Bank or US R Molecules (NIH) and like Swiss-3D-Image (University of Geneva) our IMAGE LIBRARY contains non-standard images (different rendering techniques,labeling, color coding, different views ...). Further, images of buidling blocks, like amino acids, standard and modified nucleotides, base pairs, are also available. There are many published structures obtained by modeling procedures which probably never will be included into the Protein Data Bank or Nucleic Acid Database. It would be very useful if these structures were available via the IMAGE LIBRARY OF BIOLOGICAL MACROMOLECULES. If authors are interested to provide their structures to this LIBRARY they should contact me. ====================================================================== Juergen Suehnel E-mail: jsuehnel@imb-jena.de Biocomputing URL: http://www.imb-jena.de Institut fuer Molekulare Biotechnologie Tel.: +49 (0)3641 65 6200 Beutenbergstr. 11, Postfach 100813 Fax : +49 (0)3641 65 6210 D-07708 Jena / Germany From BIOSCI-REQUEST Fri Apr 21 16:42:53 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id QAA10889 for rna-list; Fri, 21 Apr 1995 16:42:53 -0700 Received: from cgl.ucsf.EDU (cgl.ucsf.EDU [128.218.14.2]) by net.bio.net (8.6.11/8.6.6) with ESMTP id QAA10882 for ; Fri, 21 Apr 1995 16:42:47 -0700 From: schmitz@picasso.ucsf.edu Received: from dali.ucsf.edu (dali.ucsf.EDU [128.218.22.3]) by cgl.ucsf.EDU (8.6.11/GSC4.24) with ESMTP id QAA18732 for ; Fri, 21 Apr 1995 16:42:42 -0700 Received: by dali.ucsf.edu (8.6.8.1/GSC4.23) id QAA04297; Fri, 21 Apr 1995 16:42:41 -0700 Date: Fri, 21 Apr 1995 16:42:41 -0700 Message-Id: <199504212342.QAA04297@dali.ucsf.edu> To: rna@net.bio.net Subject: RNA in the Analytical Centrifuge Dear RNA-people, I am trying to determine the molecular weights of several medium RNA species (15 to 40KD) by analytical ultracentrifugation. Can somebody help me out with an approximate value for the partial molar volume for RNA or point out where experimental values of this kind have been published. Thanks a lot, Uli Schmitz ><><><><><><><><><><><><><><><><><><> Uli Schmitz, Ph. D. UC San Francisco Dept. Pharmaceutical Chemistry San Francisco, CA 94143-0446 Phone (415) 476 4378; Fax (415) 476 0688; schmitz@picasso.ucsf.edu URL http://picasso.ucsf.edu/~schmitz ><><><><><><><><><><><><><><><><><><> From BIOSCI-REQUEST Sun Apr 23 10:16:38 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id KAA08950 for rna-list; Sun, 23 Apr 1995 10:16:38 -0700 Received: from sangam.ncst.ernet.in (sangam.ncst.ernet.in [144.16.11.1]) by net.bio.net (8.6.11/8.6.6) with ESMTP id KAA08931 for ; Sun, 23 Apr 1995 10:16:32 -0700 From: santosh@physics.iisc.ernet.in Received: from soochak.ncst.ernet.in (soochak.ncst.ernet.in [144.16.11.100]) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with ESMTP id WAA21933 for ; Sun, 23 Apr 1995 22:46:16 +0530 Received: from iisc.ernet.in (iisc.iisc.ernet.in [144.16.64.3]) by soochak.ncst.ernet.in (8.6.8.1/8.6.5) with SMTP id WAA00763 for ; Sun, 23 Apr 1995 22:46:04 +0530 Received: from vigyan.UUCP by iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA07457; Sun, 23 Apr 95 22:50:47+0530 Received: by vigyan.iisc.ernet.in (smail2.3) id AA26807; 23 Apr 95 23:38:48 EDT (Sun) Received: by physics.iisc.ernet.in (Smail3.1.28.1 #6) id m0sEOqU-000BP1C; Wed, 24 May 95 22:24 GMT Message-Id: Date: Wed, 24 May 95 22:24 GMT To: rna@net.bio.net Subject: help From BIOSCI-REQUEST Sun Apr 23 11:00:03 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id LAA11165 for rna-list; Sun, 23 Apr 1995 11:00:03 -0700 Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by net.bio.net (8.6.11/8.6.6) with SMTP id KAA11131; Sun, 23 Apr 1995 10:59:52 -0700 Received: from borduas.nlm.nih.gov by ncbi.nlm.nih.gov id AA11914; Sun, 23 Apr 1995 13:59:14 -0400 Received: by borduas.nlm.nih.gov id AA15230; Sun, 23 Apr 1995 13:59:07 -0400 Date: Sun, 23 Apr 1995 13:59:07 -0400 From: francis@borduas.nlm.nih.gov (Francis Ouellette) Message-Id: <9504231759.AA15230@borduas.nlm.nih.gov> To: yac@net.bio.net, rna@net.bio.net, santosh@physics.iisc.ernet.in Subject: Re: help Reply-To: francis@ncbi.nlm.nih.gov X-Sun-Charset: US-ASCII Content-Length: 1833 > From BIOSCI-REQUEST@net.bio.net Sun Apr 23 13:18 EDT 1995 > From: santosh@physics.iisc.ernet.in > Date: Wed, 24 May 95 22:24 GMT > To: yac@net.bio.net > Subject: help The address for getting help is not that of the newsgroup, but what I show below. When you write to the newsgroup, two things happen: 1) everybody who subscribes to the newsgroup sees your message. 2) you do not get the help documentation two things you don't want! all the best, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov ================================================================ Help messages may be obtained from the BIOSCI E-mail server by sending one of these messages shown bellow to: biosci-server@net.bio.net info faq This will get you the latest FAQ for all the BIOSCI/bionet newsgroups. info usinfo This will get you the latest information sheet for subscription from the Americas and Pacific rim countries. info ukinfo This will get you the latest information sheet for subscription from Europe, Africa and central Asian countries. These message will return you the BIOSCI FAQ, and information on how to subscribe to other newsgroups from the US and UK sites (respectivly). These documents are also available via gopher: gopher net.bio.net --> 6. FAQs and Other Documents/ --> 1. BIOSCI Frequently Asked Questions. 2. BIOSCI Access for users in the Americas and the Pacific Rim. 3. BIOSCI Access for users in Europe, Middle East and Africa. 4. General Internet Information. 5. Information on USENET (1 of 2). 6. Information on USENET (2 of 2). 7. bionet-checkgroups-msg [ 3Jan95, 7kb]. and World Wide Web: http://www.net.bio.net/ ========================================================================= From BIOSCI-REQUEST Sun Apr 23 11:36:02 1995 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.11/8.6.6) id LAA12910 for rna-list; Sun, 23 Apr 1995 11:36:02 -0700 Received: from ebc.ee (tamm.ebc.ee [193.40.23.2]) by net.bio.net (8.6.11/8.6.6) with ESMTP id LAA12750 for ; Sun, 23 Apr 1995 11:33:24 -0700 Received: (from tmargus@localhost) by ebc.ee (8.6.9/8.6.9) id VAA25692 for rna@net.bio.net; Sun, 23 Apr 1995 21:31:53 +0300 Received: from mango.mef.ki.se (mango.mef.ki.se [130.237.128.18]) by ebc.ee (8.6.9/8.6.9) with SMTP id QAA15409 for ; Fri, 21 Apr 1995 16:50:09 +0300 Received: by mango.mef.ki.se (AIX 3.2/UCB 5.64/4.03) id AA16271; Fri, 21 Apr 1995 15:50:02 +0200 Date: Fri, 21 Apr 1995 15:50:01 +0200 (DFT) From: Ole Matzura Subject: RNAdraw 1.0 beta now available! To: Rnadraw Update List , Rnadraw Info list , aflaloc@bgumail.bgu.ac.il, Anders.Wennborg@mtc.ki.se, art@aars.mit.edu, c-medina@cs.uiuc.edu, ebayna@ucsd.edu, ed@molbiol.uct.ac.za, ep@info.ucl.ac.be, escriou@pasteur.fr, Giuliano@ib.pi.cnr.it, nxp3@ciddpd2.em.cdc.gov, OTELLO@sc2a.unige.ch, pp001356@interramp.com, shjang@biho.taegu.ac.kr, tmargus@ebc.ee, tracy@svm.vetmed.wisc.edu Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1917 Sender: tmargus@ebc.ee Hello there! RNAdraw is a complete RNA secondary structure/Basepair probability matrix / Heat curve calculation package for 32-bit MS-Windows. It offers an extensive easy-to-use (once you get the hang of it) interface and powerful editing/printing/calculation/analysis functions. Algorithms are based on the work of M. Zuker and J. McCaskill and were ported directly from the Vienna RNA package. RNAdraw version 1.0 beta is now available for testing and using. This version includes the following features over version 0.99-08: 1) Possibility to edit/modify/save/load all energy parameters used by the programs RNA calculational algorithms. 2) Possibility to export all RNA secondary structure / Basepair probability matrix / Probability histogram / Heat curve windows as Windows standard/placeable/enhanced metafiles. This gives a high quality possibility to import views into major word-processing/layout/DTP applications. 3) Possibility to calculate basepair probability matrixes for imported structures. 4) Lots of minor changes and new functions. 5) Extended help files. 6) etc... So why wait? RNAdraw is available either via the RNAdraw WWW homepage located at : http://broccoli.mfn.ki.se/rnadraw/rnadraw.html or via anonymous ftp at: broccoli.mfn.ki.se - in the pub/rnadraw directory. If you want direct info on updates and the RNAdraw add yourself to the RNAdraw mail list by sending you E-mail to the below address. PLEASE notify me if you have any problems or suggestions concerning RNAdraw, I really want it to be as good as possible. Good Luck! Ole Matzura ------------------------------------------------------------ Ole Matzura ole@mango.mef.ki.se Dept. of Medical Physics Karolinska Inst. Stockholm, Sweden FAX:+46-8-326505 ------------------------------------------------------------