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

Lokesh P. Tripathi lokesh at
Thu Oct 18 03:53:58 PDT 2007

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

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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