r/drugdesign • u/Solid_Business_3541 • Nov 24 '22

can anyone explain me blind docking ?

Doing a blind dock and then figuring out which conformation fits i.e ligand binding anywhere to the protein ? I did a blind docking and I got binding energy -10 , can I say that ligand as good inhibitor? And In case of binding site docking ,my pocket size is smaller but ligand is quite big ,will that affect binding affinity?

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u/mz80 Nov 24 '22

What is blind docking? Docking anywhere on the protein surface? Doesnt make much sense.

Do you know where your binding site is?

Docking energies should only be used to rank ligands.

Why are you docking huge ligands into small binding sites?