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

Kalidas Y kalidas.y at
Sun Oct 21 02:10:23 PDT 2007

Dear Lokesh

 you may set grid  center to the centre of active site like the following: (
in .gpf file)
example:  gridcenter    9.694   6.754  28.176

 To compute the center, one suggestion I have is, to obtain the xyz's of
C-Betas of site residues and compute the centroid.

With Regards

On 10/18/07, Lokesh P. Tripathi <lokesh at> 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
> ________________________________________________
> --- ADL: AutoDock List  --- ---

Thanking You
With Regards
Kalidas Y

"Love will warn you against advising another to do something that you,
yourself, do not want to do - Baba"

"You May Not Always Oblige, You Can Speak Obligingly." - Baba

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