Figure 1. Sampling of the HIV-1 protease binding pocket by ritonavir and a conserved water.

Top: One key water molecule hydrogen bonds (black lines) with both HIV-1 PR flexible flaps and protease inhibitor Ritonavir. Middle: Standard docking begins with translation of the inhibitor from its centroid, by up to 5 Å (green sphere). Protein centric water docking also includes up to 4 Å translation of water (red sphere). Bottom: Grey mesh indicates sampling space covered after ligand rotation. Image was prepared using Pymol. The structure shown was downloaded from the protein databank (PDB ID: 1HXW).