Subject: Large loop + Binding site

From: "Jianhui Wu" <[email-masked]>
Date: Fri, 26 May 2000 12:09:49 -0400

Dear All,

A couple days ago, I asked question about modelling large loop. I
received several request for the summary. Sorry folks, I have not got
any useful response yet. Maybe my question is too broad.  Let me try it
again.

To model a large flexible loop in the protein modelling is risky.
However, if the loop is found to involve with ligand binding (it
happens!), then the key step is to get a good model of the loop.
Moreover, the loop conformation usually will change on the binding of
ligand. In my case, the loop contains about 55 residues. What is the
state of the art in modelling this kind of loop? Do you know any
successful case?  I got several models of this large loop, most of them
point away from the protein surface! Any suggestion will be greatly
appreciated.

Sincerely,

Jian Hui Wu
Institute Armand-Frappier
Laval, QC