In foldit we have a BUNS filter in design puzzles, because it has not been possible to include the BUNS penalty directly in the score function. The foldit score function, like the Rosetta score function, only includes attributes of single amino acids (such as backbone angles) or pairs of amino acids (such as clashing). Anything that requires looking at more than two amino acids at a time (such as whether a polar atom is satisfied or not) has to be added as a separate bonus or penalty. Now a scientist at Baker lab has developed a way to calculate the BUNS penalty for each pair of amino acids. Hopefully this will be incorporated into foldit at some point! Then wiggle and similar tools can weigh the BUNS penalty against all the other score parts when optimizing, instead of having it as a separate (and slower) filter penalty.
Author summary from B. Coventry:
We present an algorithm that fits into existing protein design software that allows researchers to penalize unsatisfied polar atoms in protein structures during design. These polar atoms usually make hydrogen-bonds to other polar atoms or water molecules and the absence of such interactions leaves them unsatisfied energetically. Penalizing this condition is tricky because protein design software only looks at pairs of amino acids when considering which amino acids to choose. Current approaches to solve this problem use additive approaches where satisfaction or unsatisfaction is approximated on a continuous scale; however, in reality, satisfaction or unsatisfaction is an all-or-none condition. The simplest all-or-none method is to penalize polar atoms for simply existing and then to give a bonus any time they are satisfied. This fails when two different amino acids satisfy the same atom; the pairwise nature of the protein design software will double count the satisfaction bonus. Here we show that by anticipating the situation where two amino acids satisfy the same polar atom, we can apply a penalty to the two amino acids in advance and assume the polar atom will be there. This scheme correctly penalizes unsatisfied polar atoms and does not fall victim to overcounting.