ADL: Docking Entire Protein

Francois Berenger mlists at
Tue Nov 24 17:08:24 PST 2020

Maybe this might help:


On 21/11/2020 23:06, James Lloyd wrote:
> Hi,
> I am working with footprinting agents that covalently label the
> surface of a protein. By carrying out a differential binding
> experiment one can infer where ligand binding occurs.
> I would like to simulate labelling of my protein with my footprinting
> agent and how this compares to experimental data. I have a python
> script which can run multiple vina docking events using a whole
> protein grid box, which then parses these runs into a single docking
> file. I am not so concerned about individual docking events but
> rather, the global docking statistics - i.e. where my label docks to.
> I understand that AutoDock Vina was not created for such a purpose.
> Therefore I would appreciate some feedback as to the
> disadvantages/drawbacks I should be aware of when using Vina for this.
> Thanks in advance,
> James
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