They can't predict how the protein will fold because they don't understand how the folding process actually works. They just know that it will fold, and maybe they suspect a class of enzymes is a requirement for the process. The scientists looking at protein folding likely can't figure it out simply because they don't understand the fundamental nature of water and aren't even considering how it could be playing a role in the process.
Fun fact: Scientists still can't figure out how proteins are folded. They just know it happens when you add water.
Two things:
It is true that biologists cannot predict the final 3-D shape of a protein from it's linear code
As for "how" they are folded, class of enzymes named, with tremendous creativity, "foldases" do the work
They can't predict how the protein will fold because they don't understand how the folding process actually works. They just know that it will fold, and maybe they suspect a class of enzymes is a requirement for the process. The scientists looking at protein folding likely can't figure it out simply because they don't understand the fundamental nature of water and aren't even considering how it could be playing a role in the process.