From ipcakc@vigyan.ernet.in  Fri Mar 25 08:00:54 1994
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To: CHEMISTRY@ccl.net
Subject: Configuration Mixing 
Date: 25 Mar 94 15:03:25 EST (Fri)
From: ipcakc@vigyan.iisc.ernet.in
Message-Id: <9403251503.AA22735@vigyan.iisc.ernet.in>



Dear Netters,

	I am intererested in calculating the contribution of various
configurations such as (D(+)A(-)), D(*)A, (D(-)A(+)) etc. for a
metathetic reaction B---H + B-----> B---H---B ---> B + H---B and
H----B----H reactions where [D=(H-B) and A=H or B] in VALENCE BOND
mode.  Does anyone have a program to calculate the energies and wave
functions in the valence bond mode for the above mentioned configurations?
I need to know the contributions of various configurations in a 
metathetic reaction. 
	Thanks in advance and mail your answers to the following
e-mail address.

		ipcakc@ipc.iisc.ernet.in

							Sridhar.

V. Sreedhara RAo
Department of I.P.C 
Indian Institute of Science,
BANGALORE - 560 012. INDIA


From neilpaur@pipeline.com  Fri Mar 25 10:00:58 1994
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From: Neil Paur <neilpaur@pipeline.com>
Message-Id: <199403251456.JAA20382@pipeline.com>
To: CHEMISTRY@ccl.net
Subject: Looking for Ploting software (high speed) 



To: CHEMISTRY@ccl.net
Subject:  


Perhaps someone can help me.  I am looking for a plotting 
package and/or commercial tool kit which is capable of rapidly 
plotting a fairly large number of data points (100,000 - 
300,000).  I'm looking for something that will run in Windows 
3.1.  I have some concerns about a 16 bit package being able to 

plot that large a number of points.  I hope to find something 
which we can develop with and will become part of a larger 
product. The final application is chromatography.

Thanks.

neilpaur@pipeline.com

   ----- End of the message -----



From jwcnmr@watson.ibm.com  Fri Mar 25 12:00:49 1994
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Date: Fri, 25 Mar 94 11:52:29 EST
From: "James W. Cooper"          <jwcnmr@watson.ibm.com>
Reply-To: "James W. Cooper, Ph.D."          <JWCNMR@watson.ibm.com>
To: CHEMISTRY@ccl.net
Subject: Windows plotting packages
X-External-Networks: yes


Of the ones I have looked at, Origin by Microcal (Northampton MA) seems most
likely to be a candidate. I tried a few thousand points and it handled them
well, but I never tried > 100K. By contrast Jandel SigmaPlot is a very slow
performer with arrays >10 points. It just does too many repaints and does
them too slowly.



James W. Cooper
Manager of Programming and Scientific Solutions
We're not opening old Windows, we're opening new doors:
  to Fibber McGee's Closet!


From kreidler@clio.rz.uni-duesseldorf.de  Fri Mar 25 15:00:51 1994
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From: kreidler@clio.rz.uni-duesseldorf.de (Kay Kreidler)
Message-Id: <9403251918.AA11857@clio.rz.uni-duesseldorf.de>
Subject: theory of GEOMOS (QCPE #0584)
To: chemistry@ccl.net (Theochem-Liste)
Date: Fri, 25 Mar 1994 20:17:55 +0100 (MET)
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Hello netters!

Does anyone have information about references concerning the theoretical
background of the solvation in the QCPE program # 0584 (=GEOMOS). It's an
SCRF Method (perhaps the one based on Onsager's theory), but the implementation
of the cavity size is rather different from the one used in other programs
(for example Gaussian92). So, can anybody help me?

Kay.

From cmao771@charon.chpc.utexas.edu  Fri Mar 25 15:03:35 1994
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Subject: Re: CCL:2nd Order JT References
To: hyper!slee (Thomas Slee)
Date: Fri, 25 Mar 94 13:36:01 CST
Cc: chemistry@ccl.net (Computational Chemistry List)
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l
 The first derivation of the pseudo Jahn-Teller effect has been given by
  Opik and Price in 1957 (Proc. Roy. Soc. A238, 425 )    
-- 
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
Isaac B. Bersuker		 | E-mail: 
Dept. of Chemistry	         | cmao771@charon.chpc.utexas.edu
Univeristy of Texas at Austin    | Vox: (512) 471-4671
Austin, TX 78712 	         | Fax: (512) 471-8696
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 

From DSMITH@uoft02.utoledo.edu  Fri Mar 25 15:04:21 1994
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Date: Fri, 25 Mar 1994 14:55:07 -0500 (EST)
From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" <DSMITH@uoft02.utoledo.edu>
Subject: COMP Division Newsletter
To: chemistry@ccl.net
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American Chemical Society Division of Computers in Chemistry NEWSLETTER

Now that the San Diego ACS meeting is over, the COMP division is preparing
its newsletter.  It will include news from the SD meeting, news about the
upcoming ACS national meeting, and contributed articles on such topics as
the OSC mail exploder; gopher, WWW and mosaic; the Collaboratory Workshop
recently held at the Battelle PNL, mailing lists and other internet resources
for computational chemistry, and more.  If there is something you would like
to contribute please contact me directly.

Also, with this issue of the newsletter, we will be accepting product
advertisements from both large and small companies, including consulting
and R&D services.  If you have an interest in placing an ad, contact me
directly for rates and information.

When ready (approximately 1 month from now) the newsletter will be mailed
as hard copy to all COMP division members (over 2300 persons).  We also
plan to place an archive copy at the OSC chemistry mailing list archives
at some point.

Doug

Douglas A. Smith
Assistant Professor, Department of Chemistry
Center for Drug Design and Development
 and
Chairman-elect, ACS Division of Computers in Chemistry

The University of Toledo
Toledo, OH  43606-3390

voice    419-537-2116
fax      419-537-4033
email    dsmith@uoft02.utoledo.edu


From kcs2c@uva.pcmail.virginia.edu  Fri Mar 25 17:00:55 1994
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From: "Kevin C. Stewart" <kcs2c@uva.pcmail.virginia.edu>
Date: Fri, 25 Mar 94 16:50:52 EST
X-Mailer: UVa PCMail 1.8.4
To: CHEMISTRY@ccl.net
Subject: Windows plotting packages


Sorry about posting to the whole CCL, I deleted the original poster.

     Our group uses both Jandel's SigmaPlot for Windows and 3-D Vision's
Stanford Graphics Version 2.1.  In an unscientific test on a 33 MHz 486 w/
8Meg running windows 3.11 and Novell 3.11 Netware (programs and data on
network server) using a 4 column 2500 line ASCII data file it took:

                    Time to load file        Graph refresh time
SigmaPlot           ~30 sec                        ~6 sec      
Stanford            ~50 sec                        ~2 sec

     The largest files anyone uses here are ~15000  points.  There have been
complaints about the useability of both programs.

     IMHO, I think that the limiting performance factor for plotting large
data files under windows is RAM, performance plummets when Windows uses the
disk as virtual memory. My experience is that programs which are unusable
with 4 Megs are acceptable with 8 Megs and really nice with 16 Meg. (Designer
4.0, SigmaPlot, Stanford Graphics)
Kevin Charles Stewart     
Graduate Research Assistant

University of Virginia
Department of Materials Science
Thornton Hall
Charlottesville, VA 22903
 
e-mail:  kcs2c@virginia.edu 
phone:   (804) 982-5790

From aditya!raman@uunet.UU.NET  Fri Mar 25 19:00:53 1994
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Date: Fri, 25 Mar 94 15:27:17 -0800
From: aditya!raman@uunet.UU.NET (K. Ramnarayan)
Message-Id: <9403252327.AA21313@aditya>
To: uunet!ccl.net!chemistry@uunet.UU.NET, mail@uunet.UU.NET
Subject: Amino Acid Sequence Data base for Peptides?


Hello,

I am looking for a database of peptide sequences of
naturally occuring and  synthesized ones available 
so far.  Please note that my interest is only in
Linear and Cyclic peptides and not Proteins.
Is there a collection like this either 
commercially or for free?  

Please reply me directly if you can,  and I will post
a summary to the net.  Thank you very much.

Sincerely,

K. Ramnarayan, Ph.D.
email: raman%aditya@uunet.uu.net


From Bohdan.Szymanik@vuw.ac.nz  Fri Mar 25 19:04:28 1994
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From: B Szymanik <Bohdan.Szymanik@vuw.ac.nz>
Message-Id: <199403252343.AA22226@kauri.vuw.ac.nz>
To: chemistry@ccl.net
Subject: Origin and Windows Plotting


I've noted the conversation on windows plotting packages and thought I 
could add something useful. I was talking to Microcal about the 
problems of modelling backgrounds and peaks in spectroscopic data and
they said they've got a new module for integrated peak and background
fitting due to be released about now. With a new copy of Origin you
get the peak/bkgd fitting module for some special discount.

We're just going to stick with the ordinary copy of Origin. You can
write extensions to the package in a script language called LabTalk that's
kinda like an interpreted C (?). You can also interface external
precompiled routines as .dll 's. I've certainly used data sets of up to
15,000 but not so far to 100k. I've found it not to difficult to expand
on the original package. You can add windows buttons and menu items as well.

-Bohdan Szymanik
Victoria University/Industrial Research Ltd
Wellington, New Zealand

From mwd@carina.cray.com  Fri Mar 25 20:00:55 1994
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From: mwd@carina.cray.com (Mark Dalton)
Message-Id: <9403260034.AA25448@shamu>
Subject: AA sequence databases
To: chemistry@ccl.net
Date: Fri, 25 Mar 1994 18:34:33 -0600 (CST)
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This is in reply to a request on where to find the databases of
peptide sequences.  I will give a list of where to access most
databases (DNA, RNA, amino acid, etc.) That was compiled by Amos Bairoch). 
Also most of the databases are available via gopher and/or mosaic.

For primary protein sequence databases: PIR and Swiss-prot have been
the most common, there is also GenPept.  Many of the DNA sequences
will also have included with them the protein sequence.

Once you get to one Mosaic server, you are likely to find the rest
in this list and more.

Mosaic (From my hot-list):
http://www.ncbi.nlm.nih.gov/ Fri Mar 25 18:27:41 1994
The National Center for Biotechnology Information (NCBI)
http://www.gdb.org/hopkins.html Fri Mar 25 18:30:09 1994
Hopkins Bio-Informatics Home Page

http://www.genethon.fr/genethon_en.html Fri Feb 18 09:35:00 1994
Welcome to GENETHON WWW server
http://ibc.wustl.edu/ Fri Mar 25 18:24:41 1994
Washington University Institute for Biomedical Computing
gopher://ibc.wustl.edu/1 Sun Mar 13 21:28:46 1994
Div of Biology and Biomedical Sciences Research Book
http://www.nlm.nih.gov/#r&d Sun Mar 13 21:40:26 1994
HyperDOC: The National Library of Medicine (NLM)
http://golgi.harvard.edu/homepage.genome Fri Mar 25 18:26:40 1994
Harvard Biological Laboratories - Genome Research


Feel free to contact me if you have any questions/problems.

Thanks!

Mark


Below is a list of various databases available via anonymous ftp.

==============================================================================
Name   : serv_ftp.txt
Version: 1.00 / February 1, 1993
Concern: List of molecular biology FTP servers for databases and software
Author : Amos Bairoch / Dept. Medical Biochemistry / University of Geneva
         bairoch@cmu.unige.ch
==============================================================================

B) DATABASES
============

  B1) Databases abbreviations
  ---------------------------

db          Database

5S_RNA      Berlin 5S rRNA db
AIDS-db     Human Retroviruses and HIV viruses compilation of sequences
AIMB-db     Artificial intelligence and molecular biology researchers db
Alu         Alu Sequence db
Blocks      Protein blocks db
Codon       Codon usage tables for the GCG software package
CpGIsle     CpG islands in the human genome db
CCSD        Complex Carbohydrate Structure db
CUTG        Codon usage tables for all major species
DDBJ        DNA Data Bank of Japan
DSSP        Dictionary of Secondary structure of proteins
ECD         Escherichia coli db
EMBL        European Molecular Biology Laboratory nucleotide sequence db
Enzyme      Enzymes nomenclature db
EPD         Eukaryotic Promoter db
EST-db      Expressed Sequence Tag db
FANS_Ref    Functional Analysis of Nucleotide Sequences bibliography
FlyBase     Drosophila Genetic Maps db
GDB         Human Genome db
GenBank     GenBank nucleic acid db
GenPept     Automatic translation of GenBank CDS into protein sequences
HAEMB       Haemophilia B mutations db
Jour_TOC    Table of contents of some biomolecular journals
Kabat       Sequences of proteins of immunological interest
LiMB        Listing of Molecular Biology databases
NGDD        Normalized Gene Designation db
OMIM        Online Mendelian Inheritance in Man
PDB         Protein Data Bank (3D structures)
PIR         Protein Information Resource (NBRF protein sequence db)
PKCDD       Protein kinases catalytic domain db
Plsearch    Automatically generated protein sequence patterns db
Prosite     Dictionary of Protein Sites and Patterns
Rebase      Restriction Enzymes db
RepBase     Prototypic sequences for human repetitive DNA
SeqanalRef  Sequence analysis bibliography
Small_RNA   Compilation of small RNA sequences
Swiss-Prot  Swiss-Prot protein sequence db
T4-Phage    Bacteriophage T4 genome sequence files
TFD         Transcription Factors Relational db
tRNA        Compilation of tRNA sequences and sequences of tRNA genes


  B2) Major FTP servers for databases
  -----------------------------------

Organism : National Center for Biotechnology Information (NCBI)
Name     : NCBI repository
Address  : ncbi.nlm.nih.gov (130.14.20.1)
Contact  : Scott Federhen; federhen@ncbi.nlm.nih.gov

Organism : European Biology Molecular Laboratory
Name     : EMBL Anonymous Ftp Server
Address  : ftp.embl-heidelberg.de (192.54.41.33)
Contact  : Rainer Fuchs; nethelp@embl-heidelberg.de

Organism : Weizmann Institute of Science (EMBnet Israel national node)
Name     : DNA and protein sequence analysis (DAPSAS) ftp server
Address  : sunbcd.weizmann.ac.il (132.76.64.79)
Contact  : Jaime Prilusky; lsprilus@weizmann.weizmann.ac.il

Organism : Basel Biozentrum Biocomputing server (EMBnet SWISS national node)
Name     : Basel EMBNet ftp server
Address  : bioftp.unibas.ch (131.152.8.1)
Contact  : Reinhard Doelz; doelz@urz.unibas.ch

Organism : National Institute of Genetics (Japan)
Name     : National Institute of Genetics ftp server
Address  : ftp.nig.ac.jp (133.39.16.66)
Contact  : Yoshihiro Ugawa; yugawa@genes.nig.ac.jp


+-------------------------+--------+------+------+-------+-------+
|  Name                   |  NCBI  | EMBL | Weiz | Basel | Japan |
+-------------------------+--------+------+------+-------+-------+
|                         |        |      |      |       |       |
|  DDBJ                   |        |      |      |       | Yes   |
|  EMBL                   |        |  Yes |  Yes |  Yes  | Yes   |
|  GenBank                |   Yes  |      |  Yes |       | Yes   |
|  SWISS-PROT             |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  PIR                    |        |      |  Yes |  Yes  | Yes   |
|                         |        |      |      |       |       |
+-------------------------+--------+------+------+-------+-------+
|                         |        |      |      |       |       |
|  5S_rRNA                |        |  Yes |  Yes |  Yes  |       |
|  AIDS-db                |   Yes  |      |  Yes |       |       |
|  AIMB-db                |   Yes  |      |  Yes |       |       |
|  Alu                    |        |  Yes |  Yes |  Yes  |       |
|  Blocks                 |   Yes  |  Yes |  Yes |       | Yes   |
|  CpGIsle                |        |  Yes |  Yes |  Yes  |       |
|  CCSD                   |   Yes  |      |      |  Yes  |       |
|  CUTG                   |        |  Yes |  Yes |  Yes  | Yes   |
|  DSSP                   |        |  Yes |  Yes |       |       |
|  ECD                    |        |  Yes |  Yes |  Yes  | Yes   |
|  EcoSeq/Map/Gene        |   Yes  |      |      |       |       |
|  Enzyme                 |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  EPD                    |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  EST-db                 |   Yes  |      |      |  Yes  |       |
|  FANS-Ref               |        |  Yes |  Yes |  Yes  |       |
|  FlyBase                |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  HAEMB                  |        |  Yes |  Yes |  Yes  |       |
|  Jour_TOC               |   Yes  |      |  Yes |  Yes  |       |
|  Kabat                  |   Yes  |      |  Yes |       |       |
|  LiMB                   |   Yes  |  Yes |  Yes |  Yes  |       |
|  NGDD                   |   Yes  |      |      |  Yes  |       |
|  PKCDD                  |   Yes  |  Yes |  Yes |  Yes  |       |
|  Prosite                |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  Rebase                 |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  Repbase                |   Yes  |  Yes |  Yes |  Yes  |       |
|  SeqanalRef             |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  Small_RNA              |        |  Yes |  Yes |  Yes  |       |
|  T4-Phage               |   Yes  |      |  Yes |  Yes  |       |
|  TFD                    |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  tRNA                   |        |  Yes |  Yes |  Yes  |       |
|                         |        |      |      |       |       |
+-------------------------+--------+------+------+-------+------ +


  B3) Other FTP servers for databases
  -----------------------------------

Organism : University of Geneva / Medical Biochemistry and University Hospital
Name     : ExPASy server
Address  : expasy.hcuge.ch (129.195.254.61)
Databases: Enzyme, EPD, Jour_TOC, Prosite, SeqanalRef, SWISS-PROT
           Directory: /databases
Contact  : Amos Bairoch; bairoch@cmu.unige.ch

Organism : Department of Molecular biology / Massachussetts General Hospital
Address  : frodo.mgh.harvard.edu (132.183.190.10)
Databases: EMBL, Codon
Contact  : Mike Cherry; cherry@frodo.mgh.harvard.edu

Organism : University of Houston Gene-Server
Address  : ftp.bchs.uh.edu (129.7.2.43)
Databases: PIR
           Directory: /pub/gene-server/pir
Contact  : Dan Davison; dbd@theory.bchs.uh.edu

Organism : Indiana University / Biology Department
Name     : IuBio archive for biology
Address  : ftp.bio.indiana.edu (129.79.224.25)
Databases: FlyBase and various other fly databases and stock lists.
           Archive of the BIOSCI newsgroup postings (In directory:
           /usenet/bionet).
Contact  : Don Gilbert; archive@bio.indiana.edu

Organism : ?
Address  : ftp.tigr.org (192.207.234.10)
Databases: EST-db
Contact  : ?

Organism : National Library of Medicine
Address  : lhc.nlm.nih.gov (130.14.1.128)
Databases: AIMB-db
           Directory= /pub/aimb-db
Contact  : Lawrence Hunter; hunter@nlm.nih.gov

Organism : Molecular Biology Computer Research Resource (MBCRR)
Address  : mbcrr.harvard.edu (134.174.51.4) 
Databases: Plsearch
           Directory= /MBCRR-Package
Contact  : Temple Smith; tsmith@mbcrr.harvard.edu 

Organism : Human Genome Data Base / Johns Hopkins University
Address  : mendel.welch.jhu.edu (128.220.59.42)
Databases: GDB, OMIM.
Contact  : GDB User Support; help@welch.jhu.edu

Organism : Protein Data Bank (PDB)
Address  : pdb.pdb.bnl.gov (130.199.144.1)
Databases: PDB
Contact  : skora@bnl.gov.

Organism : The Salk Institute for Biological Studies
Address  : salk-sc2.sdsc.edu (192.31.153.12)
Databases: PKCDD
Contact  : Anne Marie Quinn; quinn@salk-sc2.sdsc.edu

Organism : New England BioLabs (NEB)
Address  : vent.neb.com (192.138.220.2)
Databases: Rebase
           Directory= /pub/rebase
Contact  : Dana Macelis; macelis@neb.com

Organism : NCI-FCRDC
Address  : fconvx.ncifcrf.gov (129.43.52.4)
Databases: GenPept
           Directory= /pub/genpept
Contact  : Mark A. Gunnell; gunnell@ncifcrf.gov

Organism : Pittsburgh Supercomputing Center (PSC)
Address  : ftp.psc.edu (128.182.62.148)
Databases: GenBank
           Directory= /biomed/genbank/annotated
Contact  : Alex Ropelewski; ropelews@psc.edu

Organism : BIOSCI at IntelliGenetics
Address  : net.bio.net (134.172.2.69)
Databases: BIOSCI documents (including FAQ)
           Directory= /pub/BIOSCI
Contact  : Dave Kristofferson; kristoff@net.bio.net

Organism : SERC Daresbury
Address  : s-crim1.dl.ac.uk (148.79.64.2)
Databases: Various databases and software package. Provides part of what is
           found on the EMBL and INN servers.
Contact  : Alan Bleasby; ajb@s-crim1-dl.ac.uk

==============================================================================

-- 
Mark Dalton                   AUG-GCU-AGA-AAG                  H      
Cray Research, Inc.           M   A   R   K                    |     
Eagan, MN 55121                                  CH3-S-CH2-CH2-C-COOH
Internet: mwd@cray.com                                         |   
(612)683-3035                                                  NH2

