Figure 2
From: Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction
Peptide-RMSD versus CABS-dock energy and example top ranked models obtained in CABS-dock docking.
Panel (a) shows the peptide-RMSD vs. CABS-dock energy graph for 10,000 CABS-dock models. The markers indicate the best models produced in the docking. The structures we obtained represent the p53 peptide bound close to the binding site and the receptor in the “open” conformation (b–d) and also models with the N-terminal lid docked in the binding site - the receptor in “closed” conformation (e). The receptor protein is colored from blue to red (partially visible, the lid is colored in blue), the peptide model is colored in red and the X-ray structure of the peptide is shown in magenta. The peptide-RMSDs of the models were (b) RMSD = 3.74 Å (1st ranked model), (c) RMSD = 4.36 Å (2nd ranked model), (d) RMSD = 11.26 Å (3th ranked model), and (e) RMSD = 15.79 Å (8rd ranked model).
