[Dock-fans] Fwd: Anchor Specification

Trent E. Balius tbalius at aol.com
Thu Nov 15 15:21:51 PST 2012


 

-----Original Message-----
From: Trent E. Balius <tbalius at aol.com>
To: brianfochtman <brianfochtman at gmail.com>
Sent: Thu, Nov 15, 2012 11:44 am
Subject: Re: Anchor Specification


 Hi Brian,

Yes, you can choose a rigid fragment to be the anchor during a docking run, see the "Identification of Flexible Layers" section of the Manual:

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#IdentificationofFlexibleLayers

 
excerpt: 


To use a single specific anchor (e.g scaffold with known bonding pose), specify an atom name in the chosen fragment (e.g. C16):
  user_specified_anchor yes  
atom_in_anchor C16


I would think that you will want to use this option in combination with restrained (k = 10) fixed-anchor docking.

First place the anchor on top of the crystal ligands corresponding moiety using chimera and then begin the docking.

This might be useful to the dock-fans: is it OK if i forward this to the list?

I hope this helps, 

Trent



 

-----Original Message-----
From: Brian Fochtman <brianfochtman at gmail.com>
To: Trent E. Balius <tbalius at aol.com>
Sent: Thu, Nov 15, 2012 11:15 am
Subject: Anchor Specification


Hi Trent,
   
    Hope all is going well.  I am working on a modeling project for a collaborator where I am trying to predict the binding pose of a fatty acid within a protein for which there are no ligand-bound crystal structures. 
   
    To start, I have a small molecule structure which is similar chemically to the head group of the fatty acid that I will dock in.  The protein catalyses similar reactions for both the fatty acid and the small molecule, so I will assume that the similar features of the small molecule and fatty acid will overlay.
    
   Once I get a pose for the small molecule I want to specify the atoms the small molecule shares with the fatty acid as the anchor and only sample the flexibility of the rest of the fatty acid chain.
    
   Rob seemed to think that you had a method to specify the anchor for cases such as this.  If you do could you point me in the right direction?
   
Thank you,
             Brian

 
 
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