Subject: (Fwd) CCL:side-chain replacement program

From: [email-masked] (Michael Bower)
Date: Tue, 13 Jan 1998 15:50:08 -0500 (EST)

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

	SCWRL is a very fast and reliable option - I developed it in 
Fred Cohen's lab along with Roland Dunbrack.  It uses a backbone-dependent
rotamer library and a systematic search to place sidechains, and is 
non-stochastic.  SCWRL was extensively tested against the entire database
of known structures and in the course of constructing thousands of 
homology models.  See Bower, Cohen, & Dunbrack, J. Mol. Biol. (1997)
267, 1268-1282.  

	See www.cmpharm.ucsf.edu/~bower/scwrl/scwrl.html for more 
information and ordering info.  SCWRL is free to academic researchers.

	Mike Bower

	Not speaking for SmithKline Beecham