Does the score completely ignore salt bridges, metal ion coordination, disulfide bonds, and hydrogen bonding along the side chain? These are pretty important interactions in proteins.
You are obviously more technically aware of this protein folding business then I, but I can tell you by observation that hydrogen bonds are indeed factored both in to the score, and into the behavior of the proteins, as well as shown on your display (If you chose them in the VIEW menu).
Indeed, I believe you will find puzzle 44 very interesting. It begins with a few hydrogen bonds, and you will find you don't score over about 8,900 without making many more.
We are scoring all the hydrogen bonds, although we are not showing them all, because we felt they add too much clutter to the visualization. Salt bridges are implicitly handled by the score function, and disulfide bonds are handled but currently turned off for technical reasons. We do not consider metal ion coordination.
Great info. I'm hoping to use Fold It! in my biochem class this summer, so now I'll know what to tell them.