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I'm taking an undergraduate level class on computer based drug design. The class is more for biology students than people with a strong understanding in physics and computer science.

With that said, I'm having trouble discerning the difference between what molecular docking and scoring functions are.

To me they seem like they are the same thing since they have the same goal, which is to figure out which ligands have the strongest binding affinity to a target protein. But what are the different ways each method accomplishes that and when would each method be used if (to me) each method does the same thing? Is a scoring function a way to check the validity of a docking simulation, if so how?

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