Well then lets get the ball rolling. There's a theory that protein folding is like a funnel. That is to say, the initial probability space is huge, much like the wide end of a funnel. But then it quickly collapses and the probability space becomes close enough to be computable by brute force.

Now while there are some proteins that will unfold and then fold correctly again, most can't do that. Most don't start out as one long chain that then crumples in the right shape on its own. Most are carefully built from other parts, carefully guided along the desired path of entropy. And if they misfold, and that does happen, they are taken out.

Now I personally have always thought of it as a simulation. Think about a can of mixed nuts. Have you ever noticed that the biggest kinds are always on top, and the smallest at the bottom?

You might have to shake the can for a while but they will sort by size with the biggest on top. This is a function of friction and volume. If you shake a glass jar of mixed nuts, you can almost see a flow along the sides with the smaller ones flowing down and the bigger ones "floating" to the top.

Imagine you were given the starting position of each nut, and the exact time and direction and force of the shaking of the jar. You are asked to write a simulation which will predict the final locations of each nut.

If you think about a single threaded algorithm looking at each nut and how it nudges its neighbor and its neighbor and so on, it's a lot of calculations.

But if you think of it a multi-threaded simulation then things get interesting.