not soo similar really, but yes, alphafold-style generative models could help find realistic structures for a specific composition. However a) data is much worse (I would say so at least...), b) the clever tricks of alphafold centered around strings of aminoacid don't really apply to particles in a box... and c) search space might be even larger if you go to interestingly sized systems.

Also there's been some people arguing about the particles in a box situation for a loooong time and the most promising approach currently is diffusion.