I guess this is a question for the people running this: What exactly does the score correspond to? I assume you're trying to minimize some kind of energy, but which metric do you use? Thanks.
The lower the energy required to hold the whole thing together, the more likely it is close to the natural form of the protein, and the higher your score.
This was a topic of discussion over on Rosetta@home.
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=3578
The lower the energy required to hold the whole thing together, the more likely it is close to the natural form of the protein, and the higher your score.