How does Foldit deal with Secondary Structure?
You’ve probably already noticed that any part of the puzzle can be turned into the seconday structures Loop, Helix, or Sheet without any change to your score. Yet the native Structure of that protein has clearly defined substructures that are identifiable in X-ray studies. What’s going on?
Foldit developers haven’t told us much about this, so what follows is only fugofish’s opinion. If anyone knows more about this, please update us all.
When you change a section from one structure type to another, the puzzle is static. The amino acids are in the same positions as they were before; the energy of the molecule is the same, so the score shouldn’t and doesn’t change.
When you move that section, however, the structure will try to “act” appropriately. Loop sections will be flexible and wiggly because that’s how loops are. Helix sections will be stiff because helices have internal hydrogen bonds that stabilize that shape; the program might take into account the gentle pulling of these internal bonds in helix form but ignore them in loop form. The same argument goes for sheets.
I think this is true in Rebuild, as well. If you Rebuild a section in loop form, it goes all over the place. If you Rebuild in helix form, there’s still some flopping, but the Rebuild is seeking possible helical formations, and you see more helix-like structures than you do just random structures.
I think this is why the Local Wiggle Strategy works best on loops – that section can freely seek its best conformation without the constraints that secondary structures impose.
Just one fish’s opinion.