Right. I'm actually not sure how relevant it all is to discussions of an A.I. trying to get arbitrary things done with proteins. Folding an existing protein may be a great deal easier than finding a protein which folds into an arbitrary shape. Probably not all shapes are allowed by the physics of the problem. Evolution can't really be said to solve that problem either. It just produces small increments in fitness. Otherwise organisms' proteomes would be a lot more efficient.

Although on second thought, an A.I. would probably just be able to design a protein with a massively low energy funnel, so that even if it couldn't simulate folding perfectly, it could still get things done.

Regardless, an imperfect solution would probably suffice for world domination...