I've found foldit fun, but struggled (particularly as the puzzles became more complex) with perception of the structures.

I think it might have to do with the lack of hints/depth cues. It also feels like the game makes poor use of texture features and antialiasing, something even low-end cards these days can do handily (though a manual or GUI configuration of such features would be welcome for those who have older cards and so on.)

A little more attention to visuals, like light shadowing, might go a long way?