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. 2021 Jul 15;6(29):19045–19057. doi: 10.1021/acsomega.1c02350

Figure 8.

Figure 8

RMSD plot of α-amylase protein with (Z)-octadec-9-enoic acid. The plot shows the RMSD evolution of α-amylase (left Y-axis). The ligand RMSD (right Y-axis) indicates the stability of the ligand (Z)-octadec-9-enoic acid with respect to α-amylase and its binding pocket. In the plot, Lig fit Prot shows the RMSD of (Z)-octadec-9-enoic acid when the α-amylase–(Z)-octadec-9-enoic acid complex is aligned to the protein backbone of the reference, followed by measurement of the RMSD of the (Z)-octadec-9-enoic acid heavy atoms. Values significantly larger than the RMSD of α-amylase indicate that (Z)-octadec-9-enoic diffused from its initial binding site. Stable binding was observed after 70 ns.