Protein structure prediction is now considered to be "solved," but the way it was solved was not through physics applied to what is clearly a physics problem. Instead it was solved with lots of data, with protein language modeling, and with deep nets applied to contact maps (which are an old tool in the space), and some refinement at the end.
The end result is correct not because physics simulations are capable of doing the same thing and we could check Alphafold against it, but because we have thousands of solved crystal structures from decades of grueling lab work and electron density map reconstruction from thousands of people.
We still need that crystal structure to be sure of anything, but we can get really good first guesses with AlphaFold and the models that followed, and it has opened new avenues of research because a very very expensive certainty now has very very cheap mostly-right guesses.
When it comes to very complicated things, physics tends to fall down and we need to try non-physics modeling, and/or come up with non-physics abstraction.