Subject: GOLD

From: "Ibrahim M.Moustafa" <[email-masked]>
Date: Tue, 27 Aug 2002 09:27:47 +0100

Dear CCL users,

    We are planning to by a new software for docking and we think about 
GOLD. I'm wondering if people with experience in using GOLD can tell how 
they find GOLD in their docking experiment. What is the difference between 
GOLD, Flexx and DOCK? which of them gives better results?

   Appreciating your help; all comments are welcomed.

   regards,
  Ibrahim

Ibrahim M.Mostafa
Center for Biomolecular Sciences,
Molecular Sciences Building,
North Haugh,St.Andrews,
Fife,KY16 9ST,
Scotland,U.K.
Tel.   +44-1334-467257
Fax   +44-1334-462595
e-mail: [email-masked]

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From: Szilveszter Juhos <[email-masked]>
Date: Tue, 27 Aug 2002 10:31:59 +0000 (GMT)

> GOLD, Flexx and DOCK? which of them gives better results?

There a very good papers comparing them:

Stahl & Rarey: Detailed analysos of Scoring Functions for Virtual 
Screening J. Med. Chem: 44:1035-1042 (2001)

Paul & Rognan: ConsDock: A New Program for the Consensus Analysis..
PROTEINS:47(4):521-533 (2002)

Also worth to give a look to Glide (no, I have no any connection to them):
http://www.schrodinger.com/Products/glide.html
http://www.schrodinger.com/Documents/GlideDataSheet.doc

Hope it helps:
Szilva

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From: "Ibrahim M.Moustafa" <[email-masked]>
Date: Tue, 27 Aug 2002 14:34:40 +0100

Dear CCL users,

   Here is a summary of the answers I got on my question concerning docking 
program GOLD:

The question was:

At 09:27 27/08/2002 +0100, Ibrahim M.Moustafa wrote:

> they find GOLD in their docking experiment. What is the difference 
> between GOLD, Flexx and DOCK? which of them gives better results?
>
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>
>
>
>
>

   The answers came from experts mentioning the papers:

and from the experience of people in the field they arrange the docking 
programs according to the accuracy of results in the order:

                                                                  glide > 
GOLD > Flexx > > DOCK

I think we'll go for glide.

Thanks a lot for all who answered my question.

Thanks,
Ibrahim