Figure 2

Examples of pocket detection using fpocket. top left: Rank 1 pocket on the alpha amylase (7TAA). Acarbose in surface/coloured/opaque representation, the binding site is represented as yellow transparent hull. Alpha sphere centres are depicted as small red points. top right: Rank 1 pocket of the HIV1 Protease DMP450 complex (PDB Code: 1DMP). DMP450 is depicted in grey CPK representation and the binding pocket as transparent hull. Superposed are other known inhibitors (yellow) binding in the same pocket (PDB Codes: 1Z1H, 2UY0, 2P3B). Alpha sphere centres are depicted as small interconnected spheres. Alpha spheres and the pocket are coloured according to polar (orange) and apolar (white) character. bottom left: Cyclooxygenase-2 indomethacin binding site: (red) pocket identified by fpocket,(yellow) pocket identified by PocketPicker. bottom right: Acetylcholinesterase rank 1 predicted binding pocket by fpocket. Red: pocket of the holo structure with tacrine (1ACJ), yellow: pocket of apo structure (1QIF). Pockets are represented as a hull resulting from the union of the alpha spheres.