Subject: Can Autodock3.0 reckon iron in?

From: "Mingyue Zheng" <[email-masked]>
Date: Thu, 6 Mar 2003 10:49:53 +0800

Could anyone tell me if Autodock3.0 can reckon iron in ?
The receptor active site concerned includes an iron ,one of putative ways to inhibit the enzyme is that inhibitors may replace a residue ligand to the iron,which gives a complete loss of iron and hence the loss of enzyme activity. Thus I think the interaction between iron and inhibitors can not be ignored.
If can not,which program may do this kind of docking?
Thanks in advance.
Regards.
UTF-8
**********************************************
                Mingyue Zheng
        Drug Design & Discovery Center
         SIMM,China Acadmy of Science
 294 Tai Yuan Road, Shanghai,200031 P.R.China
             Tel:021-64311833-507
        E-Mail:[email-masked]  
**********************************************

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From: "Stephan Tatzel" <[email-masked]>
Date: Thu, 6 Mar 2003 10:41:32 +0100

Yes, AutoDock 3 can recognise iron atoms. AutoGrid can recognise up to
7different atomtypes in the protein. You have to change the atomtype of the
iron from Fe to M (AutoDock 1-letter atom type code) and then define the r
and epsilon values to the appropriate values for the new atom type in the
grid parameter file.

When you use AutoDockTools to set up your dockings, the program will
automatically detect an new atomtype in your protein when loading a protein
with iron and ask you to change it to the Atomtype M and also ask for the
appropriate r and epsilon values.

For further information just look on the AutoDock homepage FAQ. There is a
short tutorial How to treat an iron atom in docking.

http://www.scripps.edu/pub/olson-web/doc/autodock/faq.html

Stephan

______________________________________

Stephan Tatzel
Institute of Technical Biochemistry
University of Stuttgart
Allmandring 31
D-70569 Stuttgart, Germany

Email: [email-masked]

----- Original Message -----
From: "Mingyue Zheng" <[email-masked]>
To: <[email-masked]>
Sent: Thursday, March 06, 2003 3:49 AM
Subject: CCL:Can Autodock3.0 reckon iron in?

> The receptor active site concerned includes an iron ,one of putative ways
to inhibit the enzyme is that inhibitors may replace a residue ligand to the
iron,which gives a complete loss of iron and hence the loss of enzyme
activity. Thus I think the interaction between iron and inhibitors can not
be ignored.
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