Fig 8. Two examples of accurately classified ligand-binding pockets.

(A and B) A GDP-binding protein, the signal recognition particle receptor ftsY from E. coli, and (C and D) a heme-binding protein, the C-terminal domain of the S. enterica PduO protein. (A and C) Experimental complex structures and (B and D) close-ups of binding sites with high-scoring class-activation map (CAM) grid points. GDP and heme are shown as green sticks colored by atom type (C–green, O–red, N–blue, P and Fe–orange), whereas grid points are represented by spheres whose size and color depend on CAM values according to the scale shown in Fig 3. Hydrogen bonds are indicated by dashed black lines. Selected binding residues are labeled and colored by the interaction type (hydrogen bond–orange, aromatic–gray, hydrophobic–blue, aromatic and hydrophobic–cyan, hydrogen bond, aromatic and hydrophobic–magenta).