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

vijaya subramanian vijaya65 at
Thu Oct 18 08:51:53 PDT 2007

You can choose the pick an atom option when you are setting up the grid using autodock tools.  Clicking on the atom of your choice would work.
Otherwise use VMD to find the coordinates of an atom in the site you are looking at.
----------------------------------------> Date: Thu, 18 Oct 2007 16:23:58 +0530> From: lokesh at> To: autodock at> Subject: ADL: Docking a protein inside a known active site/cavity in the macromolecule>> 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 --- ---

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