Excellent job Scoofy! Your answers are almost completely on the ball (even your guesses)! Can we hire you?
Anyways, choosing the best structures from the samples that we generate is the most difficult part of the protein folding problem. We attempt to use approximations of the energy of the structures to choose (low energy = good structure in general) but these approximations are not always accurate enough. We cannot compute the exact energy as it would be too time consuming, even with lots of computers!