Subject: Ask for a dock program

From: "Yun Tang" <[email-masked]>
Date: Mon, 1 Oct 2001 12:57:20 -0400

BlankDear CCLers,

I am very interested in docking a small molecule into the active site of a protein-DNA complex. The active site is supposed to be made up of part of protein, part of DNA, and Mg2+ ions. I have tried to use DOCK, AutoDock and FlexX to do it. Unfortunately, it seems that all these programs have not considered DNA and Mg2+ ions as parts of the active site or receptor yet.

I am just wondering if anybody has similar experience or knows any program to handle such docking problem. Any suggestion or advice would be highly appreciated!

Best regards,

Yun
*******************************************************************
* Yun TANG, Ph.D.                                                 *
* Laboratory of Medicinal Chemistry    Tel: 301-846-5974 (O)      *
* Center for Cancer Research                301-668-8935 (H)      *
* National Cancer Institute, NIH                                  *
* 376 Boyles Street                    Fax: 301-846-6033          *
* Frederick, MD 21702               E-Mail: [email-masked] *
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From: Oliver Hucke <[email-masked]>
Date: Tue, 02 Oct 2001 18:16:24 +0200

Dear Yun,

we use FlexX for ligand docking calculations. With this program, you can
include non protein structures as part
of the receptor. I have done so with Chlorophylls and Pheophytines and
it should be possible with DNA as well, if you  include it as
hetero-file in the rdf file (you have to convert your dna to the mol2
format for this purpose - this is documented in the manual in the
section about the receptor description file).
We also had the problem with the inclusion of mg. It could be solved by
the inclusion of the following lines in the amino.dat file
(~/flex/static_data/ dircectory):

@template _mg
atom    mg
iact	mg	-	-	-	metal	metal_sp

The MG in our pdb file was named MG2, so that we had to add the
following line to the @templates section of our receptor description
file:

MG2 * * _mg

Hope this helps. Let me know if you have further questions.

Kind regards,

	Oliver 

______________________________________

Oliver Hucke
Inst. fuer Physikalische Chemie II
Universitaet Freiburg
Albertstr. 23a
D-79104 Freiburg

Tel. :  +49-761-203-5130 (/-6179)
Fax. :  +49-761-203-6189
email:  [email-masked]
______________________________________