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. 2014 Jan 31;9(1):e87520. doi: 10.1371/journal.pone.0087520

Figure 6. Molecular dynamics of sC-PRs bound to NF.

Figure 6

Root Mean Square Deviation (RMSD) of subtype C (sC) proteases bound to Nelfinavir (NF) along 50 ns of molecular dynamics simulation. The colors are given in black, red and green for the wild-type (sC-WT), D30V (sC-D30V) and V32E (sC-V32E), respectively. Note that the sC-V32E RMSD behavior points to an open conformation state of the protease within the first 20 ns, alternating between open and closed conformation along the simulated period. The sC-WT and sC-D30V PRs remained in a closed conformation along the entire simulation.