The name of the computer program is Rosetta. It computes a "Rosetta score" that tells how properly folded a protein is as the program tries different foldings. To compute this score, the program considers the packing of amino acids within the protein according to many scoring rules. The lower (more toward the negative) the scores are, the better the folding.

The Rosetta score for the best folding that your computer has identified for a particular protein is shown as the "Min" value under the current Rosetta Score in the left half of your agent's application window. You can see snapshot pictures of the partially folded protein that your computer is working on in the right half of the window. The left side shows two other numbers that tell how properly folded the protein is thus far. The Environment score shows how well the central core of the protein has been packed together. The Pair score tells how well certain amino acids have been paired up with the correct counterparts. If a trial fold gets a worse score, then the Rosetta program tries to refold the protein a different way to see if it produces a better score. This is done millions of times for each protein. Scientists will look at the best scoring protein structures and use those in the next steps of their research.