ADL: Ensemble-based docking

James Starlight jmsstarlight at
Thu Dec 5 01:43:39 PST 2013

Dear AutoDock users!

I'm looking for the tutorial with the examples of how I could include
protein flexibility to the docking run. This time I'd like to specify not
only the flexibility of ligand-binding site residues but the ensemble of
target conformations obtaind from the molecular dynamics run (for example I
have 100 snapshots= 100 full atomic pdbs of the  protein) and 10 ligands.
I'd like to compute the affinity of the each ligands to each conformation
of the protein (it should be qual to 10*100 docking runs). How It could be
done easily ?

Thanks for suggestions,


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