Subject: RE: Docking software vithout validation

From: "Paul Hawkins" <phawkins$at$tripos.com>
Date: Thu, 26 Feb 2004 12:09:42 -0500

Szilva,

How would you judge success in such a comparison? Several criteria come to
mind;

Reproduction of rmsd of a ligand from a crystal structure?
Ranking the "native" ligand highest in a cross-docking experiment?
Scoring high affinity compounds well, and low affinity compounds poorly? Or
perhaps a good correlation between score and binding affinity?
Enriching known active compounds from a large pool of known inactive
compounds?

I look forward to your response.

Paul.

Paul Hawkins
Applications Scientist
Tripos Inc
1699 South Hanley Road
St. Louis MO 63144

Ph: 617-899-4151
E-mail: phawkins$at$tripos.com

www.tripos.com

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request$at$ccl.net]On
Behalf Of Szilveszter Juhos
Sent: Thursday, February 26, 2004 2:37 AM
To: chemistry$at$ccl.net
Subject: CCL:Docking software vithout validation

Dear All,

As flexible docking getting to be an accepted tool in virtual screening,
it is nice to see the growing number of such software available on the
market. My only problem is that most of them in the last months comes
without any validation data stating simply that "we are the champions".
It is just like walking in from the street and trying to sell something
without scientific background. Probably it works for double glazing but
I am pretty sure companies spent months with validation so I would
encourage them to publish their comparison data. It is true not only for
docking of course.

The so called "GOLD set" is more or less the "golden standard" of such
docking studies and easily available, it is even pre-processed for
docking. So please, please use it and random library sets (as used ie
with Glide) if possible.

Thanks:
Szilva

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