Subject: side-chain replacement program

From: Deepak Singh <[email-masked]>
Date: Tue, 13 Jan 1998 14:36:46 -0500

Hi everyone,
	
	I am looking for a profram or package(preferably freeware), that can I
can use to substitute various amino acids in a protein.  I am planning
to run some calculations on mutants and proteins with a lot of residue
conservation.  One way I could think of doing this would be to keep the
backbone fixed and change side chains on prompting.  Any suggestions?

Thank you

Deepak.

 ----------------------------------------------------------------------
			       Deepak Singh
                             Graduate Student
			  Department of Chemistry 
				  &
	        W. M. Keck Center for Molecular Electronics
			   Syracuse University
			   Syracuse, NY 13244

 Voice: (315) 443 5928, 443 1739                     
 email:[email-masked]
 Fax  : (315) 443 4070		        URL:http://web.syr.edu/~desingh 
 
 ......the time is gone the song is over, thought I'd something more
 to say.    Roger Waters in "time"
 -----------------------------------------------------------------------

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From: "Peter Shenkin" <[email-masked]>
Date: Tue, 13 Jan 1998 13:35:19 -0500

On Jan 13,  2:36pm, Deepak Singh wrote:
> Subject: CCL:side-chain replacement program

There are a number of programs -- commercial and academic -- that do
this.  For one of them, and a brief review of some of the others as
of the publication date, see:

	Shenkin, Farid and Fetrow, "Prediction and Evaluation of
	Side-Chain Conformations for Protein Backbone Structures,"
	Proteins, v.26, pp.323-352 (1996)

(If you're interested in using "side", the program described there,
let me know; the source code is freely available.  But be warned:
it's not terribly user-friendly.)

	Hope this helps,
	-P.

-- 
************ I have never seen even one episode of "Seinfeld." ************
* Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 *
** NY, NY  10027;  [email-masked];  (212)854-5143;  FAX: 678-9039 ***
*MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html *

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From: Pieter Stouten <[email-masked]>
Date: Tue, 13 Jan 1998 14:48:47 -0500

>backbone fixed and change side chains on prompting.  Any suggestions?
Try Whatif. It is free for academia. It can systematically replace
individual residues and tell you how well the mutated residue fits into the
rest of the structure (it does not optimize the structures when doing that,
though). Contact Gert Vriend <[email-masked]>, Whatif's
author, directly for more info.

Good luck,

Pieter Stouten <[email-masked]>
DuPont Merck - Computer Aided Drug Design Group
Web: http://www.halcyon.com/stouten/

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From: Pieter Stouten <[email-masked]>
Date: Tue, 13 Jan 1998 15:22:40 -0500

On 98/01/13 at 14:48 -0500, I wrote:

>Try Whatif. It is free for academia.
>
I just got set straight: in principle it is about $200 for academia to
cover  S&H, administrative overhead, etc. I think this is a one-time fee
that entitles you to receiving future upgrades free of charge. Please
contact Gert Vriend for the official word.

Pieter Stouten                              ||
Computer Aided Drug Design Group            ||  No good deed ever
The DuPont Merck Pharmaceutical Company     ||   goes unpunished
P.O. Box 80500, Wilmington, DE 19880-0500   ||
Phone: +1 (302) 695 3515                    ||  (Ferengi Rule Of
Fax: +1 (302) 695 9090                      ||  Acquisition #285)
Internet: [email-masked]    ||
Web: http://www.halcyon.com/stouten/        ||