Subject: Validating docking codes.

From: "Mark Thompson" <mark-.at.-arguslab.com>
Date: Tue, 27 Apr 2004 21:18:10 -0700

I have a new docking code and scoring function that I'm currently
validating.  I'm mainly using the data in Wang's J. Med. Chem paper (2003,
46, 2287-2303) and the Gold test set.  I've culled most of the docking
literature for other "standard" tests.

One area where I'm weak is having good ligand libraries for testing database
enrichments.  I could construct these libraries myself, but then direct
comparisons with other docking/scoring methods cited in the literature might
be ambiguous.

I would appreciate hearing from anyone who knows of any such data sources
that are available to the public.

Cheers,
Mark

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

mark-.at.-arguslab.com
http://www.arguslab.com
***************************

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From: Szilveszter Juhos <szilveszter.juhos^at^chemaxon.hu>
Date: Wed, 28 Apr 2004 09:59:28 +0200

> comparisons with other docking/scoring methods cited in the literature might

You are right, however, in the recent Glide paper (J. Med. Chem. 2004, 47,
1750-1759 by  Halgren et al.) they are using the same ACD set that was
used by Bissantz et al. (J. Med. Chem. 2000, 43, 4759-4767) as far as I
see. My opinion ACD is really not the best source of lead/drug-like
entities. The FlexX people (J. Med. Chem. 2001, 44, 1035-1042)  used a
subset of WDI. Having WDI (means having $$$) you can make some
comparison though it is only the library creation process not the
entities you can read from the article. 

Likely the best thing you can do is to generate your own libs
in the same way as it was mentioned in the papers. OTOH, testing with
1000 or so non-native ligands is not necessarily enough: using vHTS usually
the top 1% or less of the whole library is purchased and that is the
first ten if you are using a 1K lib :/

Cheers:
Szilva