mbinfield Lv 1
There might be another problem with the scoring function, along the same lines as the issue with design puzzles favoring the large aromatic side chains.
From what I've read, serine is considered a structure-breaking amino acids and does not normally show up in sheets or helices. So, if serine doesn't belong in a beta sheet in nature, I wouldn't expect the mutate function to be substituting it into beta sheets very often. However, I've noticed that in freestyle design I'm often getting serine in my beta sheets. If it were just one or two, that would be realistic, but I'm looking at a ten-segment beta strand with four serines, and in one case recently I had a sheet that was almost entirely serines. That can't be right.
