I know that blind docking is most often used to determine an unknown binding site, but can it be used to determine whether a ligand is thermodynamically more likely to bind a given (known) binding site instead of another site on the target protein?
In other words, here's my thinking: if I dock a library of ligands in a given binding site, the program (VINA in my case) will give me the best poses for that particular binding site, but it won't tell me if there's a more energetically favorable site elsewhere on the protein. By doing blind docking first, I can see if the top-scoring poses for each ligand are in the given pocket or elsewhere on the protein and thus screen for ligands that are more likely to bind in a given pocket. Is this a valid rationale for starting with a blind docking even when the binding site is known?
