Isolating significant cavity regions with Boolean Set operations. A. A diagram of Boolean Set operations, showing the borders of input regions (dotted) and output (solid), in grey. B,D) Polygons representing regions occupied by protein x (blue) and protein Y (red), their molecular surfaces (black lines), and their binding cavities x (light blue) and y (light red). C) Superimposition of x and y, based on a whole structure alignment of X and Y. In E, F, and G, the superposition of x and y is depicted as dotted lines. Regions in solid lines were computed with Boolean set operations. E) The difference of x and y. F) The intersection of x and y. G) The difference of y and x. H) Statistically significant fragments from E and G. I) Statistically insignificant fragments from E and G.