An In Silico Analysis of the Binding Modes and Binding Affinities of Small Molecule Modulators of PDZ-Peptide Interactions
Figure 12
Comparison before and after MD (PDZ3).
(A) Structural superimposition of docked complex of one of the ligands (3,4-dichlorophenylethylATAV) before and after MD simulation on 3rd PDZ domain of PSD-95 protein (PDBID: 1BE9) where the ligand is moving out of the binding pocket of the 1BE9 during the course of simulation. (B) Structural superimposition of docked complex of one of the ligands (AnthracenethylETAV) before and after MD simulation on 3rd PDZ domain of PSD-95 protein (PDBID: 1BE9) where the ligand is repositioning itself in the binding pocket of the 1BE9 during the course of simulation.