(A) Plot of root mean square deviation (RMSD) of Cα of NEMO/IKKβ (protein) and NEMO/IKKβ/WA (complex). RMSDs were calculated using the initial structures as templates. For protein (red) the reference is the PDB structure and for complex (blue) the reference is the initial model. The trajectories were captured every 1 ps until the simulation time reached 2600 ps. (B) Plot of total energy of NEMO/IKKβ and NEMO/IKKβ/WA (complex) The energy trajectories of both the protein (red) and the complex (blue) are stable over the entire length of simulation time.