I recently did docking using PyRx program, and noticed that docking multiple ligands simultaneously gives slightly different binding energy for some of the ligands compared to when each of the ligands are docked against same receptor.
Also, I observed that the interacting amino acids also differ in some ligands in the two cases.
Thanks.
This could be due to that the program uses different starting positions for the ligands in the simultaneous docking case, which could lead to different conformations and interactions with the receptor. It is also possible that the ligands are competing with each other for the same binding site, which could affect their binding energy and interacting amino acids.
Good luck.
I will agree with the first explanation of @Hamed Shahriarpour. However, his second explanation looks invalid. While we can analyze multiple ligands, there is no competing interaction between the ligands. By the time the analysis of the first ligand ends, the binding side returns to default with no information about the first ligand.
Pyrx is a great program
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