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Figure 11
Results of MD simulations. Summary of the key geometric analysis performed along the MD trajectories for both the active (PDB entry 6y2e) and new-inactive (PDB entry 7nij) conformations of SARS-CoV-2 Mpro. (a) and (b) highlight the time-dependent variation of the protein root-mean-square deviation (r.m.s.d.) of Cα atomic positions for PDB entries 6y2e and 7nij, respectively. (c) and (d) summarize the per-residue mean root-mean-square fluctuation (r.m.s.f.) of atomic positions of protein Cα atoms for PDB entries 6y2e and 7nij, respectively. The most relevant regions of the protein are highlighted in the plot for visualization clarity as described in the legend. For both r.m.s.d. and r.m.s.f. analyses, each chain composing the crystallographic dimer is considered separately.

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