Figure 4
From: Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction
Analysis of lid dynamics.
(a) Above diagonal - intramolecular contact map for the MDM2 protein in CABS-dock docking representing averaged frequencies of intra-protein contacts of the MDM2 protein in the docking simulation (comprising 10,000 models); below diagonal - native intramolecular contact map for the MDM2 protein based on the crystallographic structure (PDB ID: 1T4F). The green and blue bars along the axes mark the lid and binding site regions of the receptor, respectively. (b) RMSF (root-mean square fluctuation) averaged over the trajectory from the CABS-dock simulation (blue line). The grey rectangle shows the area investigated so far with all-atom MD (reported in refs 25,31, 32, 33, 34). The rectangle borders show the maximal RMSF value obtained and the largest MDM2 fragment included in these simulations.
