With regards to protein-ligand interactions, we talk about two concepts, docking and scoring. I understand that docking means to find the best orientation of a ligand at the active site of a protein, and scoring is to compare several docked ligands to see which ligand best binds to the protein.
To quote this paper,
"While there is now a general consensus that most of the popular docking algorithms perform fairly well in generating sound poses, scoring functions most often fail to adequately evaluate the binding affinity."
What does it mean to be docked, if not being the pose with the best binding affinity? If not, how is docking done without calculation of binding affinity?