CCL: Loop prediction - reconstruction of protein missing residues

From: Ben Webb <ben~~salilab.org>
Subject: CCL: Loop prediction - reconstruction of protein missing residues
Date: Thu, 09 Mar 2006 09:31:41 -0800

 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. Amissing residues example is athttp://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