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. 2021 Jan 25;11:592908. doi: 10.3389/fmicb.2020.592908

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Copyright © 2021 Eweas, Alhossary and Abdel-Moneim.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Ligand/protein complex MD simulation: selected examples. (A) Remdesivir/spike (t = 0): spike closes, (B) Remdesivir/spike (t = 13 ns), the spike opens, and the ligand is still in place, (C) Lopinavir/PLpro (t = 0), the ligand is in place, (D) Lopinavir/PLpro (t = 26 ns), the ligand left the pocket. (E) Remdesivir/PLpro (t = 0), the ligand is in place, (F) Remdesivir/PLpro (t = 23 ns), the ligand moved to the other side of the pocket, (G) Remdesivir/NP (t = 2 ns), the ligand is in the pocket, (H) Remdesivir/NP (t = 21 ns), the pocket is obliterated, and the ligand left the pocket, but it is still attached to the receptor with two hydrogen bonds, and one Pi stacking, (I) Remdesivir/NP (t = 22 ns), the pocket is still obliterated, and the ligand left the pocket, but it is still attached to the receptor with one hydrogen bond. (J) Remdesivir/NP (t = 30), The pocket is open again and the ligand is restored in place.