Subject: Summary: DNA model building software

From: Masayuki Yuki <[email-masked]>
Date: Wed, 30 Aug 95 11:00:29 PDT

Dear CCL Subscribers:

I would like to thank everyone who responded to my question regarding the
availability of DNA model building software.  I learned that there are many
commercial/academic softwares that I can either purchase of obtain through
ftp.

Here are the responses that I received so far:

Date: Thu, 24 Aug 95 16:15:45 PDT
From: [email-masked] (Tom Macke)

I have an experimental code that has been used to build all sorts of helices,
hairpins, pknots, etc.  It is structure decription language that allows you
to build these molecules by a combination of rigid body transforms, distance
geometry and if you have an AMBER license, molecular mechanics.  Version 1.0
is on our anon ftp:

	ftp scripps.edu
	login as anon, etc

	cd /pub/macke
	binary
	get nab.XXXXX.tar.Z

Version 1.1 with several functional improvements will be posted to the ftp
on Monday 28 Aug.  The new documentation approaches useable.

The code called nab, compiles structure description programs into C which the
user executes to create the structures. Runs on sun4SunOS4, sun4SunOS5, IRIX5,
IRIX6, hp-ux, titan3000 and Convex.  Will not run on MS boxes.  Requires a
C compiler (GNU-C will do).  

nab can generate AVS modules allowing real time (depending on size) interactive
structure creation, where the paramters of the model are attached to AVS dials
and buttons.  Open Inventor Version planned, but must graduate first.  If this
seems interesting, let me know.

tom

Date: Fri, 25 Aug 1995 10:32:24 +0100 (BST)
From: James Crabbe <[email-masked]>
To: Masayuki Yuki <[email-masked]>

The Windows version of DeskTop Molecular Molecular Modeller will fit the 
bill - cost about $250.  It has been well reviewed (e.g. JACS), and is 
available from Oxford University Press - see the back cover of J. Mol. 
Graphics latest version.
Contact Mary Levine, OUP, Madison Ave., New York.  email [email-masked], 
fax : 212-726-6450.

James Crabbe

From: Andreas Goeller <[email-masked]>
Date: Fri, 25 Aug 95 12:42:03 METDST

Just have a look at the home page (see below). There is the access to
the Oxford Molecular home page.

				Bye, AHG...

---------------------------------------------------------------
   Andreas Goeller               Computer Chemie Centrum der
   Dipl.-Chem.    	        Universitaet Erlangen/Nuernberg
                                      Naegelsbachstr. 25
phone: +49(0)9131-856583               D-91052 Erlangen 
  fax: +49(0)9131-856565                   Germany
email: [email-masked]      
http://www.organik.uni-erlangen.de
---------------------------------------------------------------

Date: Fri, 25 Aug 95 17:03:12 -0400
From: [email-masked] (Joel Polowin)

As long as you can specify the torsional angle values, you can build it
with HyperChem.  The standard nucleotide database has the usual residues;
it's easy to add your own.  Standard conformations are A, B, and Z; or you
can specify "other" and fill in the required angles.  Single- and double-
strand are standard options; for other strandedness you'd have to build the
extra strand(s) and move them into place.  DNA and RNA are standard in the
builder.  The software runs under Windows 3.1 and our tests so far under
beta-test Win'95 have beem positive; we'll have a version for SGI IRIX 5.3
(if you're thinking of upgrading) by the middle of September.

I can send you more information and/or demo disks if you want; info and
demos are also available from our WWW server, http://www.hyper.com .

Regards,
Joel

------------
Joel Polowin, Ph.D.   Manager, Scientific Support
Email to: [email-masked] 

Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: [email-masked]    Support questions to: [email-masked]
Email group: Send "subscribe hyperchem" to [email-masked]
WWW: http://www.hyper.com/

From: [email-masked] (Alan M. Mathiowetz)
Date: Mon, 28 Aug 1995 07:39:23 -0500 (EDT)

You should contact David Case of Scripps.  He has a program Nucleic Acid
Builder which does most of the things you want.  I do not have his phone
number, but you might be able to find it through the Web at 
http://www.scrips.edu/

Date: 	Mon, 28 Aug 1995 09:27:23 -0700
From: "Mark Hanning-Lee" <[email-masked]>

 Reply to:     RE>CCL:DNA Modeling Software

Just a thought: if you want to run software on SGI, you should upgrade your
operating system. Irix 4.0.2 is years old; do yourself a favor and upgrade to
the latest version (5.3 I think). Call 1 800 800 SGI1 (or perhaps 1 800 800
4SGI). You may find it worth your while to get a support contract which lets
you get free operating system upgrades etc.

Good luck with SGI!

Mark

From: [email-masked] (Gene Carter)
Date: Tue, 29 Aug 1995 11:08:50 -0600 (MDT)
Cc: [email-masked]

The program NAMOT is capable of generating A,B. and Z forms  of DNA
as well as triplex and tetraplex. NAMOT is unable efficeintly model single
stranded reigons which, of course, rules out generation of structures 
such as hairpins.

The web site for this program is:
http://synapse.lanl.gov/~namot

Hope this helps.
Gene

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-   Group t-10 LANL                     |Los Alamos, NM 87545             |
===========================================================================

Sincerely,

Masayuki Yuki
USC School of Pharmacy Graduate Program
[email-masked]