One thing that has become apparent in CASP9 is that the top ranking foldit score is not necessarily the protein structure that is closest to the native structure. As measured by the GDT (global distance test), some of the lower scoring proteins have higher ranking GDTs. How correlated are score and GDT? Is it .98 or is it .15? If the correlation is low, then are we really working on the right problem here?
In foldit, we are trying to maximize foldit score, which is to say minimizing the energy score. If, however, a lower energy score is not indicative to being closer to the native structure, are any of the things we coming up with really of use?
In CASP9, the foldit team is submitting the top 5 scoring proteins on each puzzle. Could it be that the 10th highest scoring protein has the highest GDT? Or the 50th?