Figure 8
Molecular dynamics analysis Receptor ligand poses as obtained by docking simulations of 2870 in (A) BRD4(1) and (B) EGFR TKD and primary receptor ligand interactions (H-bonds, hydrophobic, ionic, water bridges) of 2870 for the duration of the MD simulations with (C) BRD4(1) and (D) EGFR TKD respectively.
The top panel in (C, D) shows the total number of specific contacts the protein makes with the ligand over the course of the trajectory. The bottom panel shows which residues interact with the ligand in each trajectory over time. Some residues make more than one specific contact with the ligand, which is represented by a darker shade of orange, according to the scale to the right of the plot.
