From owner-chemistry-!at!-ccl.net Thu Mar  9 13:57:01 2006
From: "Ben Webb ben+/-salilab.org" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: Loop prediction - reconstruction of protein missing residues
Message-Id: <-31164-060309130953-10603-N+Lfd4vB2BgofbuTa2uMmw,,server.ccl.net>
X-Original-From: Ben Webb <ben~~salilab.org>
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Date: Thu, 09 Mar 2006 09:31:41 -0800
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Sent to CCL by: Ben Webb [ben-$-salilab.org]
Nuno Loureiro Ferreira nunolf**ci.uc.pt wrote:
> I have some structures that I want to add some missing loops and
> reconstruct some protein missing residues (these ones at the
> terminals of the protein) .
> 
> My aim is to obtain the whole protein. I'm not so worried about if
> the loop predictions are in close agreement with known loop
> structures. Just want to make sure that the added residues/loops are
> in good stereochemical conditions without steric clashes with
> neighbouring residues.
> 
> I'm searching for Linux or SGI software that could do the job. Want
> to here some feedback on this subject, before choosing the soft pack.

You could use Modeller (http://salilab.org/modeller/) to achieve this. A 
missing residues example is at 
http://salilab.org/modeller/wiki/Missing_residues

	Ben
-- 
ben{}salilab.org                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle