Subject: AutoDock / amino-aromatic H-bonds

From: "jfbaker" <[email-masked]>
Date: Thu, 18 May 2000 22:28:33 -0500

Dear CCL subscribers,

We've been using AutoDock 3.0 to do enzyme-ligand docking simulations with
compounds which contain aromatic substituants (such as 3-phenylpropyl
groups).  We suspect that weak  "amino-aromatic" and "aromatic-aromatic"
hydrogen-bonds are important in the binding of these compounds to the active
site of our enzyme.

Since the pi-faces of aromatic substituants in the ligand aren't directly
associated with an individual atom, it's difficult to see how AutoDock can
be made to understand the location and directionality between them and
hydrogen-N(sp2) donors in the active site.

Has anyone figured out a way to get AutoDock to include these types of
non-classical hydrogen-bonds in it's H-bond calculations?

Thanks very much for any help you can provide us with...

Sincerely,

Jerry Baker     [email-masked]

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