Ensemble docking allow to dock a single ligand or a ligand library against multiple conformations of a single receptor.
Now, imagine we have a group of proteins which are functionally conserved and share similar ligand/s. Moreover, they are highly similar in the structures (Identity rate in AA level is more than 90%) and almost a perfect superimposition of 3D structure can be made by different tools.
Docking analysis was performed for each protein solely and as expected the binding pocket and residues are similar.
Now here is the question: Can we perform Ensembled docking for this situation?
Usually "ensemble" means "configurational ensemble," i.e., a collection of configurations of a single system (topology), with the configurations differing only in atomic coordinates. But technically, yes, one can make an ensemble of different systems and dock into them -- if the structures (and pharmacophore features) align well . . .
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