You are correct. I don't have timne to go into great deal right now, but briefly we are using a third energy function which is similar to the 'Bryant' one we used before but seems to work better. We also look at how compact the structures are and at how much secondary structure they have compared to that predicted (those helices and sheets (arrows) that you see in the results section are 'secondary structure' and help determine the fold of the proteins - their location can be predicted with some degree of accuracy from just the protein sequence). Thus we are combining several factors to attempt to pick out the best structures from the set we generate. We won;t know for sure if we picked the best though.