We discussed in some of the puzzle comments that having alanine-rich helices may form a good, tight core, but they are not so good in other ways.

There are times when I am working a design puzzle where an alanine seems to be exactly what I need for what I'm trying to attempt. Do I really need to take a fifty point penalty for adding an alanine to my design, when it is the most common amino acid in helices?

I propose keeping a penalty function for alanines in a helix, but only if the helices contain over a certain percentage (5%? 10%) of alanines. Who's with me on this? Hit the up arrow button, below.