I have a large collection of "3 D type" puzzles. I strongly believe they develop a "sense" of thinking in 3 space.
(Remember Star Trek 2 .. Khan was defeated 'cause he was a 2 Dimensional thinker (g))
One puzzle that I think is most relevant to protein people is the Rubik's Snake (available from puzzle stores both on and off the web) The is a primarily linear arrangement of geometric shapes that can be folded into a globular sphere. A most useful visualization aid for thinking about folding.
Compute long and prosper,