Figure 1
From: Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction
Comparison of MDM2-p53 experimental structures (a) and CABS-dock simulation models (b). Panel (a) shows NMR structures of the MDM2 receptor in the unbound form (colored from blue to red, PDB ID: 1Z1M) together with the experimental X-ray structure of the p53 peptide (colored in magenta, PDB ID: 1T4F; note that the X-ray structure of the MDM2 is highly similar to the ordered portion of its NMR ensemble presented in the figure). Panel (b) shows an ensemble of 10,000 CABS-dock simulation models of the MDM2 receptor (left), and predictions of the peptide structure (right), together with the experimental p53 peptide structure (colored in magenta). Two peptide predictions are shown: the top scored (pink color, peptide-RMSD: 3.74 Å) and the closest to the experimental structure (red color, peptide-RMSD: 2.67 Å).
