[Dock-fans] anchor orientation

Sudipto Mukherjee sudmukh at yahoo.com
Tue Apr 27 12:08:47 PDT 2010


Hi,

We actually call it "Fixed Anchor Docking", as in the ligand anchor position is fixed to the 'correct' location, and the torsions are grown out.

Regards
Trent E. Balius
Sudipto Mukherjee



________________________________
From: Dariusz Ekonomiuk <ekodarek at icm.edu.pl>
To: Trent E. Balius <tbalius at aol.com>
Cc: dock-fans at mailman.docking.org
Sent: Tue, April 27, 2010 1:26:08 PM
Subject: Re: [Dock-fans] anchor orientation


Thank you Trent
"Fix Anchor Docking" is what I was looking for.

best,
  Dariusz

>
>
>  Hi Dariusz,
>
> You can turn off ligand orientation by the following:
>
>   orient_ligand    no
>   flexible_ligand  yes
>
> This will grow out your ligands starting from the anchor in your beginning
> orientation.
> In the Rizzo group, we call this procedure Fix Anchor Docking.
>
>
> Note that the anchor will still move because of the simplex minimizer.
>
> I hope this helps,
>
>
>
> Trent E. Balius
> Graduate Student, Rizzo Group,
> Department of Applied Mathematics and Statistics,
> Stony Brook University.
> Office: Math Tower 3-129, Phone: (631) 632-8519
> URL: http://www.ams.sunysb.edu/~tbalius/
>
>
>
>
>
> -----Original Message-----
> From: Dariusz Ekonomiuk <ekodarek at icm.edu.pl>
> To: dock-fans at mailman.docking.org
> Sent: Tue, Apr 27, 2010 5:10 am
> Subject: [Dock-fans] anchor orientation
>
>
> Dear all,
>
> I have a question related to anchor and grow algorithm as implemented in
> DOCK 6.3.
> Would it be possible to use user defined orientation of the anchor ?
> In other words, I would like to start with predefined coordinates of the
> anchor and then use DOCK
> for growing the layers.
> I assume it would require modifications in the source code,
> any hints ?
>
> best,
> Dariusz Ekonomiuk
>
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> Dock-fans mailing list
> Dock-fans at mailman.docking.org
> http://mailman.docking.org/mailman/listinfo/dock-fans
>
>
>


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