Subject: change upon binding

From: Rowyna <[email-masked]>
Date: Wed, 24 Apr 2002 23:06:36 +0800

Dear CCLers,

I have a question regarding Autodock. I had a crystalised
protein-ligand complex, in which I took out the ligand and docked it
with Autodock. THe results have been consistent with the crystal
structure. But when I used a different ligand for docking, the results
are not quite as expected. I believe that the conformation of the
binding site has been shifted favourable to the original ligand and so
therefore, as autodock treats the protein rigid, the prediction of the
interactions with a different ligand is not a good. Has anybody been
through this sort of problem? I'd love to hear some opinions on it.
Actually, I'd like to find out how the binding of the another ligand
affects the conformation of the binding site, and I can't quite do it
with autodock. So, I am giving molecular dynamics a try. If there's
somebody who encountered something like this before, would be glad to
hear your input.

I've learned a lot from the mailing list so I thank all of you for your
help.

Rowyna K.