From chemistry-request@ccl.net Thu Sep  2 22:35:01 2004
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Reply-To: <mark*at*arguslab.com>
From: "Mark Thompson" <mark*at*arguslab.com>
To: <chemistry*at*ccl.net>
Subject: Limits on number of rotatable bonds in ArgusDock?
Date: Thu, 2 Sep 2004 20:44:11 -0700
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I've been asked by more than one user if there is a limit on the number of
rotatable bonds for docking molecules using the ArgusDock engine.

The short answer is : no

There is no fundamental limit in the program for max torsions, or the like.
However, I have not extensively tested drugs with numbers of rotatable bonds
> 30.  There may be some combinations of these ultra large drugs with large
shallow binding sites on the surfaces of proteins that make ArgusDock
choke....let me know if you find any.

This is one reason I put the GADock code into ArgusLab alongside the
ArgusDock engine.  GADock is pretty robust and you might find it works well
for some cases.  The ArgusDock engine has been rung-out extensively  on
hundreds of test cases, but I would still classify it as a work in progress
simply because it's not yet had widespread use from the general community.

Cheers,
Mark

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Mark Thompson
Planaria
PO Box 55207
Seattle, WA  98155
voice: 206.240.4769
FAX: 206.440.3305

mark*at*planaria-software.com
http://www.planaria-software.com
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