An In Silico Analysis of the Binding Modes and Binding Affinities of Small Molecule Modulators of PDZ-Peptide Interactions
Figure 7
The binding modes of the ligand 3,4-dichlorophenylethylATAV to the 2nd and 3rd PDZ domains of PSD95 as predicted by docking and MD simulations. The residues of the PDZ domains, which are in contact with the inhibitor for more than 50% of the simulation time during last 1ns of the 5ns MD simulations, are shown in RED color.