An In Silico Analysis of the Binding Modes and Binding Affinities of Small Molecule Modulators of PDZ-Peptide Interactions
Figure 10
Comparison before and after MD (PDZ2).
(A) Structural superimposition of docked complex of one of the ligands (PyrenbutylETAV) before and after MD simulation on 2nd PDZ domain of PSD-95 protein (PDBID: 1QLC) where the ligand is moving out of the binding pocket of 1QLC during the course of simulation. (B) Structural superimposition of docked complex of one of the ligands (3,4-dichlorophenylethylETDV) before and after MD simulation on 2nd PDZ domain of PSD-95 protein (PDBID: 1QLC) where the ligand is repositioning itself in the binding pocket of 1QLC during the course of simulation.