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Old 10th November 2021, 07:31 PM   #302
Puppycow
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Originally Posted by Chris_Halkides View Post
There is another problem with his analysis. I assume that the reaction in question is

L + R ---> L•R

where L is the ligand (the inhibitor), and R is the receptor in the broad sense of the term (which could be one of the proteases). The complex between the inhibitor and the protease is L•R. If my assumption is correct, the value of -9.9 (which is for remdesivir binding to PLPro, as shown in Table 2 of this link, the paper on Ilimaquinone) is actually the strongest binding.
EDT
The authors wrote, "Remdesivir showed the lowest binding energy and highest docking score of −9.9 kcal mol−1 which was followed by ilimaquinone having the second highest binding energy of −8.1 kcal mol−1." I infer that they authors use of the word "lowest" means "most negative." This might confuse the unwary; Dr. Campbell says that remdesivir doesn't work very well in this analysis (starting near the 14;20 time in the video). I would also point out that remdesivir is not thought to be a protease inhibitor; it is believed to work by interfering with the replication of RNA.
Yeah, I did have the impression that he might be completely misunderstanding the significance of that quote he pulled.

Is lowest binding energy good or bad? It also had the "highest docking score". And from the paper it looked like they were talking different docking sites.
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