ADL: Docking a protein inside a known active site/cavity in the macromolecule

Fred Reynolds freynolds1 at
Thu Oct 18 04:27:59 PDT 2007

Hello Lokesh

I typically open the PDF file as a text document and look at the XYZ  
coordinates of the residues of interest, and center the grid there.   
The size of the grid could be determined by looking at all the  
residues of interest, and determining the boundaries of the active  

Fred III

On Oct 18, 2007, at 6:53 AM, Lokesh P. Tripathi wrote:

> Greetings Autodockers
> I have been facing a particularly frustrating problem with  
> Autodock. My
> macromolecule is a serine protease (trypsin), where I know that the  
> active
> site cavity is constituted by residues 189-192, 214-216 and 224-228. I
> wish to dock my inhibitor protein (41 residues long) into this active
> site. But I am at loss on what to do to ensure that my inhibitor is  
> docked
> inside the macromolecule active site cavity.
> Currently the procedure I have opted for includes computing and  
> centering
> AutoGrid chemical affinity and electrostatics maps on my macromolecule
> with 126 × 126 × 126 grid points at a spacing of 1 Å.  However, as  
> you can
> expect the process is highly computationally intensive forcing me  
> to look
> for better alternatives. I can reduce the grid points and resort to
> default spacing of 0.375 A, but that does not resolve the primary  
> issue of
> ensuring that the docking is directed in the vicinity of the active  
> site.
> The best thing would be to narrow the GRID parameters to the region  
> around
> the active site only. The ADT tutorial provides X,Y,Z coordinates that
> would center the grid around the hsg (HIV protein provided for  
> testing)
> active site. I would like to know how can I determine the X,Y,Z
> coordinates that would center the grid around the active site of my
> macromolecule.
> Does anyone have an experience with this kind of a problem? Any
> suggestions on how to go about it?
> Lokesh Tripathi
> NCBS, Bangalore
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