Just a nitpick, we typically call it a local minima, because we are trying to minimize energy. A stable protein will be at (or near) the minimal energy conforma

Just a nitpick, we typically call it a local minima, because we are trying to minimize energy. A stable protein will be at (or near) the minimal energy conformation. Otherwise, I think you are absolutely correct. It's a nearly infinite computational problem that has a tendency to overfit. There are all sorts of ways to try to solve this problem, but they don't always work as well in all cases.