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Date: Mon, 6 Oct 1997 19:31:08 -0400 (EDT)
From: Peter Palenchar <pmp@udel.edu>
To: rna@net.bio.net
Message-ID: <Pine.SOL.3.96.971006193019.5477A-100000@copland.udel.edu>
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	Does anybody know where I can down load 3-D crystal structures of
tRNAs from

				Peter Palenchar




From BIOSCI-REQUEST  Mon Oct  6 17:35:08 1997
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To: rna@net.bio.net, pmp@udel.edu
Subject: tRNA structures
From: francis@ncbi.nlm.nih.gov
X-Sun-Charset: US-ASCII


> From pmp@udel.edu Mon Oct  6 19:41:33 1997

> 	Does anybody know where I can down load 3-D crystal structures of
> tRNAs from
> 
> 				Peter Palenchar

There are some in PDB (which is miss-called because it had nucleic acid
and protein structures, albeit mostly proteins).  These can be looked
at with Cn3d (NCBI's 3D structure viewer).

Starting at this URL:

http://www.ncbi.nlm.nih.gov/Structure/


I queried with "Transfer Ribo-Nucleic Acid" and obtained the 8 hits
shown bekow.  With Entrez' structure division (MMDB) browser you can
see the Medline/Pubmed links, and nucleotide sequences.  You can save
the structures in a variety of formats.

cheers,

f.

--
| B.F. Francis Ouellette  
| GenBank Coordinator
|
| francis@ncbi.nlm.nih.gov   



   6TNA 
     Transfer Ribo-Nucleic Acid (Yeast,Phe),tRNA [3348]
     (View Structure Summary,7 MEDLINE links, or 1 nucleotide link ) 

   4TRA 
     Transfer Ribo-Nucleic Acid (Yeast,Phe),tRNA [3227]
     (View Structure Summary,9 MEDLINE links, or 1 nucleotide link ) 

   4TNA 
     Transfer Ribo-Nucleic Acid (Yeast,Phe) tRNA [3224]
     (View Structure Summary,5 MEDLINE links, or 1 nucleotide link ) 

   3TRA 
     Transfer Ribo-Nucleic Acid (Yeast,Asp) tRNA (B FORM) [3117]
     (View Structure Summary,8 MEDLINE links, or 1 nucleotide link ) 

   2TRA 
     Transfer Ribo-Nucleic Acid (Yeast,Asp) tRNA (A FORM) [2961]
     (View Structure Summary,8 MEDLINE links, or 1 nucleotide link ) 

   1TRA 
     Transfer Ribo-Nucleic Acid (Yeast, Phe), Trna [2366]
     (View Structure Summary,4 MEDLINE links, or 1 nucleotide link ) 

   1TN2 
     Pb(II)-Transfer Ribo-Nucleic Acid (Yeast,Phe) tRNA (pH 5.0) [2335]
     (View Structure Summary,2 MEDLINE links, or 1 nucleotide link ) 

   1TN1 
     Pb(II)-Transfer Ribo-Nucleic Acid (Yeast,Phe) tRNA (pH 7.4) [2334]
     (View Structure Summary,2 MEDLINE links, or 1 nucleotide link ) 

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Date: Tue, 7 Oct 1997 18:41:09 -0400
From: william@amber.biology.gatech.edu (William S. Hayes)
Message-Id: <9710072241.AA24162@intron.biology.gatech.edu>
To: rna@net.bio.net
Subject: UPDATED CONF NOTICE: Gene Discovery in silico Nov 6-9 1997

			
	
	GEORGIA TECH INTERNATIONAL CONFERENCE IN BIOINFORMATICS

			GENE DISCOVERY IN SILICO
                         
			  NOVEMBER 6 - 9, 1997

                                ATLANTA

The focus of the conference is on gene identification 
and prediction of protein function using computer methods.


SPONSORS: 

Georgia Tech College of Science
Parker H. Petit Institute for Bioengineering and Bioscience at Georgia Tech
SmithKline Beecham
Gene Pro, Inc.
Glaxo-Wellcome
 

DATES:

     Early registration ends:
          October 9, 1997 

Conference schedule:

     Registration opens at 6:00pm on Thursday, November 6,
          (with the reception at 8:00pm).
     The program starts 8:00am Friday, November 7 
          and ends at noon Sunday, November 9.


LOCATION:

     The conference will be held at
     Renaissance Atlanta Hotel Downtown  
     located near the center of 1996 Olympic development,
     close to Fox Theatre & Georgia Tech  
      
     
AGENDA:

The conference agenda includes plenary talks (50 minutes for each 
talk and discussion) as well as poster session and round table discussion.

WWW page now contain all titles as well as abstracts of the 
majority of the plenary talks.

 http://intron.biology.gatech.edu/~william/conference.html

---------------------
Evening - Nov 6
Reception

Morning - Nov 7
Peer Bork	       	EMBL, Heidelberg & MDC, Berlin, Germany
		Predicting function from sequence
Geoff Barton	       	University of Oxford, Oxford, UK & EBI, Cambridge, UK
		Treading the benchmark tightrope: Making progress
		by measuring the accuracy of sequence analysis algorithms
Jim Fickett	       	SmithKline Beecham, King of Prussia, PA
		Analysis of Transcriptional Regulatory Regions
Michael Zhang	       	Cold Spring Harbor Lab, Long Island, NY
		On A New Strategy of Promoter Recognition

Afternoon - Nov 7
Pavel Pevzner	       	University of Southern California, Los-Angeles, CA
		The Twenty Questions Game with Genes
Steven Salzberg	       	Johns Hopkins University, Baltimore, MD
		Decision Trees and Markov Chains for Eukaryotic Gene Finding
Steven Henikoff	       	Fred Hutchinson Cancer Research Center, Seattle, WA
	Blocks-based methods for detecting homology and inferring function
Stephen Altschul       	NCBI/NIH, Bethesda, MD
		More BLAST for Your Buck

Late afternoon - Nov 7 (17:30 - 19:30)
 Poster Session 

Morning - Nov 8
Soren Brunak	       	Technical University of Denmark, Copenhagen, Denmark
		DNA Structure and Sequence Periodicity in Human Promoters
Sam Karlin	       	Stanford University, Stanford, CA
		Codon biases and gene clusters
Jean-Michel Claverie   	Struct & Genetic Information, CNRS, Marseille, France
		Self-identification of protein coding region in bacterial
		genomes
Mark Borodovsky	       	Georgia Institute of Technology, Atlanta, GA
		Three steps to complete gene identification in a new
		 bacterial genome with GeneMark^3

Afternoon - Nov 8
Philipp Bucher	       	ISREC, Lausanne, Switzerland
		Using generalized profiles for functional annotation
		of genome sequences
Michael Gribskov       	San Diego Supercomputer Center, San Diego, CA
		Pattern Recognition Tools for Protein Sequences
Gary Stormo	       	University of Colorado, Boulder, CO
		Combining various types of evidence to predict
		gene structures
Eugene Koonin	       	NCBI/NIH, Bethesda, MD
		A genomic perspective on protein families

Late afternoon - Nov 8 (17:30- 19:30)
Round table discussion 
- "Annotating genomes 
Rapid first pass annotation of large scale sequences"
 

Morning  - Nov 9
Terry Gaasterland      	Argonne National Lab & Univ of Chicago, Chicago, IL
		Automated Analysis of Whole Genomes: Experiences and Lessons
Anthony Kerlavage      	The Institute for Genomic Research, Rockville, MD
		Gene Finding and Functional Identification in Prokaryotic
		and Eukaryotic Genomes
Roderic Guigo	       	Inst Municipal d'Investigcio Medica, Barcelona, Spain
		Integrating multiple evidence to predict and annotate
		genes in genomic sequences
Victor Solovyev        	Amgen, Inc., Thousand Oaks, CA & Sanger Centre, UK
		A new version of GeneFinder for analysis of genomic
		DNA with multiple genes


STEERING & PROGRAM COMMITTEE:

Mark Borodovsky, Co-Chair, 	Georgia Tech
Soren Brunak			Technical University of Denmark 
Jim Fickett			SmithKline Beecham 
Eugene Koonin, Co-Chair, 	NCBI/NIH 
                 

GEORGIA TECH ORGANIZING COMMITTEE:

Chair 
	Prof. Mark Borodovsky, School of Biology & Mathematics

Advisory board
	Prof. Leonid Bunimovich, School of Mathematics
	Prof. Shamkant Navathe, College of Computing

Poster session
	Dr. Alex Lukashin, School of Biology, 

Publicity
	William Hayes, School of Biology, 
	william@intron.biology.gatech.edu

Registration and general events
	Laura Olson, Department of Continuing Education, 
	laura.olson@conted.gatech.edu
	Bonnie Griffin, School of Mathematics
	griffin@math.gatech.edu

        We thank Dr. Sorin Istrail and Dr. Ying Xu for help 
        in compiling the e-mail distribution list. 

POSTER SUBMISSION

     To apply for participation in a poster session, 
     please send the title and one page abstract of your poster, 
     by October 3, to Dr. Alex Lukashin, 
     by e-mail: lukashin@amber.biology.gatech.edu (preferred method) 
     or by FAX: (404) 894-0519.

     You may send the abstract earlier. The acceptance of the high
     quality poster will be confirmed within five days upon submission.

REGISTRATION

     Registration Fee:

          Early (until October 9) $295, Academic/government - $245
          Late: $345, Academic/government - $295

     The registration fee includes handout materials and meals provided by
     Renaissance hotel chefs for the whole conference time. 


Hotel Reservations:

     This conference will be held at the Renaissance Atlanta Hotel
     Downtown. 

     Call Renaissance Atlanta Hotel 404-881-6000 for reservation with Georgia  
     Tech room rate of $99/night by October 3, 1997. Please mention the 
     Bioinformatics/Georgia Tech conference.


Travel Discounts:

     Delta Air Lines offers special fares to attendees of Georgia Tech
     programs. Certain restrictions may apply. For information and
     reservations, call 1-800-241-6760 and refer to file U0175 (for
     domestic flights only).
 
 
To obtain more information & the registration form, visit the WWW page: 		
     http://intron.biology.gatech.edu/~william/conference.html

or contact us by 

e-mail:		register@conted.swann.gatech.edu

Phone:		(404) 894-2400 

Fax:		(404) 894-8925

From BIOSCI-REQUEST  Thu Oct  9 02:00:09 1997
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Date: Thu, 9 Oct 1997 02:00:06 -0700
From: BIOSCI Administrator <biohelp>
Message-Id: <199710090900.CAA09917@net.bio.net>
To: rna@net.bio.net
Subject: BIOSCI/bionet miniFAQ & Fundraiser

(LAST REVISION: 30-JUL-95)

This BIOSCI "miniFAQ" is designed to answer the questions that come up
the *most frequently*.  The main BIOSCI FAQ (Frequently Asked
Questions) is accessible on the World Wide Web at URL
http://www.bio.net/.

If you can not find an answer to your question in this or other
documentation, the BIOSCI technical support staff answers e-mail
queries sent to

		       biosci-help@net.bio.net

We can only answer questions about the use of the newsgroups and
mailing lists.  We unfortunately do not have the staff to do Internet
information searches or answer scientific questions.  Please post
those to the appropriate BIOSCI/bionet newsgroups.


	Contents:
	--------
	0) BIOSCI NEEDS YOUR SUPPORT!!

	1) Using the WWW to access the BIOSCI/bionet newsgroups.

	2) What to do about "spams," i.e., junk mail, ads, etc.

	3) Examples of subscribing and unsubscribing to the mailing lists.

	4) The BIOSCI user address and research interest directory.


0) BIOSCI NEEDS YOUR SUPPORT!!
------------------------------
BIOSCI's government funding has been expended, and we are now
operating solely from advertising revenue that we have raised from our
Web site at http://www.bio.net/.  We need just a few minutes of your
time to help us serve you.

You can do two important things which will take very little time for
you individually and will immensely help us continue to help you.

First, please use our WWW system at http://www.bio.net/ to access the
archives.  You can post or reply to messages via your Web browser as
described in item #1 below.  Your usage helps attract sponsors. If you
contact any of our sponsors, please be sure to thank them for
supporting BIOSCI. It is critical for them to get this feedback if
they are to continue their sponsorship for the long term.

Second, if you work for a company or organization that provides
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this message on to your marketing or marketing communications
department or other appropriate group.  Please ask them to help
support BIOSCI by sponsoring our Web site and explain the uses and
benefits of the system to the biology community. If they are
interested, they can then contact us for further information at our
tech support address, biosci-help@net.bio.net.


1) Using the WWW to access the BIOSCI/bionet newsgroups.
--------------------------------------------------------
As of 10 December 1995, all BIOSCI/bionet full newsgroups are
accessible through the World Wide Web (WWW) at URL http://www.bio.net.
One can read and reply publicly or privately to both recent postings
and archived messages through one's Web browser if it is configured
properly to send e-mail.  Each newsgroup is equipped with its own WAIS
index.  The main BIOSCI home page also has access to the BIO-JOURNALS
Table of Contents database WAIS index and the BIOSCI user address
database described in another item further below.


2) What to do about "spams," i.e., junk mail, ads, etc.
-------------------------------------------------------
BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups),
mailing lists, and a hypermail archive at URL http://www.bio.net/.
The same postings are distributed on all media (except for a small
number of mailing-list-only groups at net.bio.net).  Unfortunately it
is becoming a despicable practice on the Internet (by a few people out
to make a fast buck) to do automated mass postings to thousands of
newsgroups and mailing lists.  These attempts to grab free advertising
are refered to as "spams" in the usual, somewhat boneheaded, net
terminology.  USENET is more susceptible to this practice, and many
spams originate on the USENET groups and then are passed on to the
mailing lists.  However, spammers also get lists of mailing addresses
and hit these too, so neither medium is immune.

What should you do personally if you get junk mail?
---------------------------------------------------
Just delete it and move on without reading it further.  Filing a
protest is becoming increasingly useless because spammers are often
disguising the addresses where the messages are sent from.  Unless you
really understand Internet mail systems, your attempt at protest by
sending replies to the message will often end up being sent to the
address of an innocent person that the spammer is victimizing.

What can BIOSCI/bionet do to protect its newsgroups?
----------------------------------------------------
The only solution currently available is to moderate the newsgroup.
If this newsgroup is already moderated, then you are in good shape.
Moderation protects the USENET distribution from about 95% of the
spams that are being sent to date and protects the mailing lists
completely.  Moderation means, however, that someone has to take the
time to review each message before it goes out.  We have set up
software here that simply allows the moderator to forward to an
address at net.bio.net messages that (s)he wishes to have distributed.
This takes no more time than that needed to read the message and pass
it on, say about 1 min. per message.

Most newsgroups currently have a discussion leader who is responsible
for their newsgroup.  The discussions leaders and their e-mail
addresses are listed in the BIOSCI Information Sheet which is
available on the Web at http://www.bio.net/.  If a newsgroup is being
hit with too many junk postings, please contact the discussion leader
for that group and see if there is interest in moderating the group.
Please do not assume that by simply posting a complaint to the
newsgroup itself, anyone on the BIOSCI staff will act on your
complaint.  With close to 100 newsgroups to run, the BIOSCI staff has
to rely on the discussion leaders of each newsgroup to report problems
directly to us at biosci-help@net.bio.net.

We will moderate any of our newsgroups if the discussion leader tells
us that the readership of the group wishes to do so and if a moderator
is willing to do the work.  For most BIOSCI/bionet groups, this
entails only a few minutes of work each day.

Moderating a newsgroup will resolve probably 95% of the junk postings
on the USENET distribution.  Unfortunately there are easy ways for
determined spammers to override the moderation mechanism on USENET,
but we can protect our e-mail subscribers from unwanted postings if
the newsgroup is moderated.  You can also access our newsgroups over
the WWW at URL http://www.bio.net.  While this Web interface will not
stop spammers from trying to post to the groups, this will give you
yet another way, besides using USENET news, to keep the junk out of
your personal mail files.  For those of you with local USENET news
systems, the Web interface will also give you faster access to new
newsgroups and recent postings.


3) Examples of subscribing and unsubscribing to the mailing lists.
------------------------------------------------------------------
PLEASE NOTE: The BIOSCI management does NOT act on
subscription/unsubscription requests that are posted improperly to the
newsgroups and mailing lists.  People who do this only bother everyone
on the lists to no avail.  Please be sure to follow the proper
procedures below.

Gory details are in the BIOSCI Information sheets on the Web at
http://www.bio.net.  Below we give an example utilizing the
METHODS-AND-REAGENTS list at both of our two BIOSCI sites:

Users in the Americas and Pacific Rim countries who use the BIOSCI
------------------------------------------------------------------
node at computer net.bio.net:
----------------------------

A) Determine the "listname" which is the <=8 character mail address
                                         ^^^^^^^^^^^^^
   for the group.  These can be found in the BIOSCI Info. Sheet.  For
   the METHODS-AND-REAGENTS group the mailing address is
   methods@net.bio.net.  The listname is the portion of the address to
   the left of the @ sign, i.e., "methods".  The listname is used with
   the "subscribe" and "unsubscribe" commands illustrated below.

B) Mail all commands in the body of a mail message addressed to
   biosci-server@net.bio.net.  Do NOT send commands to the newsgroup
   posting addresses!  Leave the Subject: line blank, any text on it
   will be ignored.

C) In the body of your message put one or more of the following
   commands with an "end" command on the last line, e.g.,

   subscribe methods
   unsubscribe methods
   end

   Do NOT put your e-mail address or other text on these lines.  The
   server only allows you to cancel your subscription if the address
   on your mail header matches the address on our mailing list.
   Please ask for help at biosci-help@net.bio.net if your address has
   changed, e.g., if you know you are on the list but the server tells
   you that you are not a member.


Users in Europe, Africa, and Central Asia who use the BIOSCI node at
--------------------------------------------------------------------
computer daresbury.ac.uk (also known as dl.ac.uk):
-------------------------------------------------

To subscribe and unsubscribe to/from the BIOSCI lists, you need to
specify the full USENET newsgroup name with "bionet-news." prepended.
The USENET newsgroup names are listed in the BIOSCI Information sheet
on the Web at http://www.bio.net/.  For the METHODS-AND-REAGENTS list
the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the
appropriate commands are

    sub bionet-news.bionet.molbio.methds-reagnts

    unsub bionet-news.bionet.molbio.methds-reagnts

These commands are included in a message addressed to mxt@dl.ac.uk,
NOT to the newsgroup mailing addresses.  As usual, include the text in
the body of the message as text on the Subject: line is ignored.

To unsubscribe from all the lists at the UK node, use

    unsub bionet-news

Please note that if the address in the list is different than the one
in your mail message header, you will not be able to unsubscribe by
this method. If you have problems, please mail biosci@daresbury.ac.uk.


4) The BIOSCI user address and research interest directory.
-----------------------------------------------------------
Please take this opportunity to add your name, address, and research
interest information to the BIOSCI User Address Database if you have
not already done so.

You can fill out the address form directly through our Web page at URL
http://www.bio.net/adrform.html.

The address database is reindexed nightly for WWW access (the URL is
http://www.bio.net/).  If you are not directly on the Internet but can
reach it by e-mail, please use our waismail server to access the user
directory.  waismail use is described above.  You can also request a
user address form by e-mail from biosci-help@net.bio.net.

Please check your database entry from time-to-time to see if your
address information is still up-to-date.  Because of our limited
personnel resources, we ask that you resubmit a *complete* form to
revise your entry; we only replace complete entries and do not have
resources to edit old forms.


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Date: Fri, 10 Oct 1997 17:29:49 -0700
From: Eugene Kolker <eugene@genome.biotech.washington.edu>
Message-Id: <199710110029.RAA21574@genome.biotech.washington.edu>
To: rna@net.bio.net
Subject: Recomb98 deadline: Oct 20


		 	 CALL FOR PAPERS
              SECOND ANNUAL INTERNATIONAL CONFERENCE ON                
                   COMPUTATIONAL MOLECULAR BIOLOGY

                           (RECOMB 98)

                       March 22 - 25, 1998  
                          New York City                   
                                                                  
                           Sponsored by 
                 Association for Computing Machinery 
                              SIGACT

                         with support from
                          SLOAN Foundation 
                      US Department of Energy
 
	      http://www.mssm.edu/biomath/recomb98.html


The Second Annual Conference on Research in Computational Molecular 
Biology (RECOMB 98) will be held in New York City, March 22 - 25, 1998. 
Papers reporting on original research (both theoretical and experimental) 
in all areas of computational molecular biology are sought, including 
surveys of important recent results/directions. Typical but not exclusive 
topics of interest include: 

- Genomics
- Molecular sequence analysis
- Recognition of  genes and regulatory elements
- Molecular evolution
- Protein structure
- Combinatorial libraries and drug design


ABSTRACT SUBMISSION: 
Authors are requested to send 10 copies (preferably two sided copies) of a
detailed extended abstract (5-10 pages)  to: 

                        Professor Pavel Pevzner
                        RECOMB 98 Program Chair
                        University of Southern California
                        Department of Mathematics, DRB 155
                        Los Angeles, CA 90089-1113

An abstract must be received by October 20 (!), 1997. This is a firm deadline. 
Simultaneous submission to another conference or journal is allowed.

For more information please visit the conference web page:
http://www.mssm.edu/biomath/recomb98.html

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Date: Mon, 13 Oct 97 00:16:45 EST
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From: Eugene Kolker <eugene@genome.biotech.washington.edu>
Message-Id: <199710132049.NAA13012@genome.biotech.washington.edu>
To: rna@net.bio.net
Subject: Recomb98 deadline: Oct. 20


		 	 CALL FOR PAPERS
              SECOND ANNUAL INTERNATIONAL CONFERENCE ON                
                   COMPUTATIONAL MOLECULAR BIOLOGY

                           (RECOMB 98)

                       March 22 - 25, 1998  
                          New York City                   
                                                                  
                           Sponsored by 
                 Association for Computing Machinery 
                              SIGACT

                         with support from
                          SLOAN Foundation 
                      US Department of Energy
 
	      http://www.mssm.edu/biomath/recomb98.html


The Second Annual Conference on Research in Computational Molecular 
Biology (RECOMB 98) will be held in New York City, March 22 - 25, 1998. 
Papers reporting on original research (both theoretical and experimental) 
in all areas of computational molecular biology are sought, including 
surveys of important recent results/directions. Typical but not exclusive 
topics of interest include: 

- Genomics
- Molecular sequence analysis
- Recognition of  genes and regulatory elements
- Molecular evolution
- Protein structure
- Combinatorial libraries and drug design


ABSTRACT SUBMISSION: 
Authors are requested to send 10 copies (preferably two sided copies) of a
detailed extended abstract (5-10 pages)  to: 

                        Professor Pavel Pevzner
                        RECOMB 98 Program Chair
                        University of Southern California
                        Department of Mathematics, DRB 155
                        Los Angeles, CA 90089-1113

An abstract must be received by October 20 (!), 1997. This is a firm deadline. 
Simultaneous submission to another conference or journal is allowed.

For more information please visit the conference web page:
http://www.mssm.edu/biomath/recomb98.html


Special thanks to William Hayes for his help in compiling the mailing list. 
Sorry, if you get this e-mail twice.

