Figure 6.

Ligand flipping during 6 μs MD simulations. Minimum distances between a nitrogen atom in the ligand (indinavir) and the catalytic residues His41/Cys145 are plotted. These distances reflect binding pose of the ligand, and thus flipping events are visualised as a sudden switching of these distances. Inset shows ligand poses at 1.0, 2.4, and 5.0 μs, where surfaces of the active site are coloured as in Fig. 5.