An In Silico Analysis of the Binding Modes and Binding Affinities of Small Molecule Modulators of PDZ-Peptide Interactions
Figure 6
RMSD vs Time plot after excluding certain residues.
(A) RMSD vs time plot for one of the MD simulations (simulation 2 from Figure 5B) on the docking complex involving the inhibitor 3,4-dichlorophenylethylATAV and 1QLC. RMSD has been calculated after excluding residues 12–15 from N-terminal and loop regions comprising of residues 42–49 & 65–70. The inset picture shows the superposition of the docked complex before and after MD. (B) RMSD vs time plot for one of the MD simulations (simulation 1 from Figure 5A) on the docking complex involving the inhibitor 3,4-dichlorophenylethylATAV and 1BE9. RMSD has been calculated after excluding residues 1–10 from N-terminal and 100–115 from C-terminal of the protein. The inset picture shows the superposition of the docked complex before and after MD.