Figure 7.

(a) Three-dimensional structure of the protein–ligand complex, 4IVB. The protein is depicted in a cartoon (green), and the ligand is depicted in color-coded ball-and-stick. Atom colors: gray (carbon), red (oxygen), and blue (nitrogen). (b) Knowledge-based estimation of protein–ligand interactions. Hydrogen bonds are depicted in red dashed lines, and hydrophobic contacts are depicted in gray dashed lines. (c) Heat map for the atomic contributions on the prediction of K_d, obtained from the LRP on PotentialNet. (d) Heat map for the atomic contributions on the prediction of K_d, obtained from the LRP on InteractionNet. The contributions are illustrated with color intensity of red (positive influence), white (zero influence), and blue (negative influence) colors.