Examples of retrieved binding pockets. The proteins shown on the top at each panel are the query protein and the bottom row shows the proteins that were retrieved at the top rank by Patch-Surfer from the database. A, a pair of AMP binding proteins and their binding pockets, 1khtB and 3kd6A. B, FAD binding proteins, 3grsA and 2gqu. C, NAD binding proteins, 1mewA and 2i65A. The color of the patches shows corresponding matched patches from the two pockets.