Figure 5
From: Modeling the binding of diverse ligands within the Ah receptor ligand binding domain
Ligands are gathered into three groups that were defined by the occupancy of different sites inside the AhR cavity and by characteristic residue interactions during MD simulations. (a) Per-residue decomposition of ΔGbind. Values were obtained as averages of the last 8 ns of simulation. In the plots, only residues lining the internal cavity are shown. (b) Ten snapshots sampled during the last 8 ns of simulation are shown for each ligand belonging to the three groups; ligands are represented as sticks.
