ADL: Dock on the exact binding site

[kanika sharma]

Hello all


There is a small ligand (straight chain 6 carbon atoms) and I have a
modelled structure for the receptor and its a GPCR.

By some in vitro studies I know where the ligand should bind. As described
by many people in the adt vina manual, I generated the grid that has centre
close to the binding site and is extended enough so that it includes enough
search space. Along with that I kept these residues of the binding site as
flexible. Also, the ligand has flexible bonds.

Now, the problem is, the ligand never binds there but goes everywhere else.
Is there a method to direct the binding to these residues? I am curious why
ligand wouldn't bind at this site in any of the docking.


Please excuse me if its too naive or non coherent

Best,
Kanika
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[jpc356]

In AutoDock Vina, I do not believe there is a function to "force" what you're describing. In AutoDock, you can create a covalent map and force it to bind to one macromolecule atom. Check the PDB file for residues that look incorrect (usually at the bottom - or with the highest integer) For example, my last PDB had GDP1998 which occupied the pocket I wanted to bind to. It is necessary to delete these atoms before attempting to run AutoDock/Vina.

Also, I don't believe this is the case, but you may be restricting the search space too much or have the exhaustive-level too low. Please look into both of these possibilities and report back if the issue persists.