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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?

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    $\begingroup$ This may not be the right place to ask this question (it's more a biochemistry question), but my take is that docking is a geometric problem: Which ligand fits geometrically onto which protein. On the other hand, scoring is about how closely they bind. Just because you can fit a round peg into a square hole doesn't mean you've already figured out how tightly it sits there. $\endgroup$ – Wolfgang Bangerth Apr 28 at 19:19
  • $\begingroup$ This question would be of interest on the new Materials Modeling SE: materials.stackexchange.com $\endgroup$ – Tyberius Apr 29 at 1:58

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