ADL: Ligand docking to MD ensemble

Oleg Trott trott at
Wed Apr 9 09:07:48 PDT 2014


People have been doing this for a while now, such as with the Relaxed
Complex Scheme. The FightAIDS at Home project is using it with Vina in


On Wed, Apr 9, 2014 at 5:16 AM, James Starlight <jmsstarlight at> wrote:
> Dear AutoDock users!
> I'm looking for the Autodock tutorial where I could  find brief description
> of how protein flexibility from the MD simulation could be take into
> account during the docking run. For instance I have ligand and ensemble of
> conformations  in dcd or pdb format corresponded to the fragment of my MD
> trajectory. Now I'd like to dock my ligand to each of that conformation in
> its pre-defined active site and find to what conformation from ensemble my
> ligand has higher affinity. I'll be thankful for any suggestions.
> Thanks for suggestions,
> James
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Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

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