[gmx-users] Ligand Binding to Homodimeric Proteins

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 18 02:48:19 CET 2010

Nancy wrote:
> Hi All,
> I am performing molecular docking simulations of a ligand binding to a 
> homodimeric protein, to determine potential binding site(s).  Due to the 
> symmetrical nature of a homodimer, I would expect that the binding 
> site(s) on one protomer would be identical on the other protomer.  
> Therefore, a ligand should bind with equal probability and affinity to 
> both sides of the protein.  However, when I perform a molecular docking 
> simulation (using an X-Ray crystal structure), the ligand preferentially 
> binds to one side of the homodimer.
> Is this outcome likely the result of errors inherent in the X-Ray 
> crystal structure, as one would expect identical binding to both sides?

This question has nothing to do with Gromacs, and as such, this is the wrong 
forum.  You should probably consult whatever support you have for whatever 
docking software you are using.

One consideration that comes to my mind is whether or not your docking target 
(e.g., the defined box in the case of AutoDock) encompasses both binding sites, 
and whether or not this is even meaningful.  But again, you're asking your 
question in the wrong place.


> Thank you very much.
> Nancy


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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