This is a suggestion for puzzles that are without a Native:

I would best define a "ghost region" as a collection of points in 3-dimensional space, where the Native conformation is likely to be, relative to the denatured protein. As players progress in the game, players tend to make "beneficial" movements which help their scores increase. These "movements" in space can be mapped and correlated into a shadow guide, for other players to work on and further refine it. This method may not allow players to converge on the "best" possible conformation, but it will help FoldIt realize one of the best of many-possible Native structures.