Subject: Large loop modelling

From: "Jianhui Wu" <[email-masked]>
Date: Wed, 24 May 2000 15:56:20 -0400

Dear all,

I am building a protein with a big loop (around 55 residues).
Experimentally, the loop was found to involve with ligand binding (that
is, some of the loop residues are in the ligand binding sites).
Moreover, the conformation change on ligand binding involve at least 10
residues. My objective is to get a model of the complex. Obviously, to
get a good model of the loop is the key step. What is the best method to
model the big loop that involve with ligand binding? By the way, the
template has similar loop but the X-ray structure do not have
coordinates for that since the loop is too flexible. I read somewhere
that people are developing method to model this kind of loop. I just can
not find it now. Can you point me to some related references?

Thanks a lot,

Jian Hui Wu
Institute Armand-Frappier
Laval, Quebec
email:  [email-masked]