Figure 2.

Changes in the pattern of flexibility in the interaction between the spike protein–ACE2 receptor complexes for Omicron and WT. The root-mean-square fluctuation (RMSF) of the protein Cα atoms with the respect to the initial structure for the evaluated spike protein–ACE2 complex was obtained by molecular docking. The spike protein–ACE2 receptor complexes were evaluated using the CABS-flex software [28]. The PDB files were submitted to the CABS-flex server to further assess the stability of the spike protein mutants–ACE2 complexes, and the parameters were adjusted to the default. The MD simulations output data obtained with both software were analyzed according to RMSF. This software enables an efficient modeling procedure for short simulations, being able to produce an analysis of the protein dynamics consistent with the dynamics obtained from 10-nanoseconds MD simulations with the most popular force fields.