I need to clarify this from those who are familiar with PyRx0.8, Autodock4 and Autodock Vina. What is the actual unit of the values generated from PyRx automated molecular docking, binding affinity (BA) (in kcal/mol), or binding energy (BE)? In Autodock4 and Autodock Vina it is BE. The panel below (see picture) reveals BA for the "scores" of the 9 poses. However, the docking results table above, which shows the top pose in Picture (with RMSD=0), has BE. I ran across discussions here in RG that BA and BE do not always match, and that there has to be some sort of "normalization/conversion" needed to transform one to the other. In the case of PyRx0.8, is it BA and BE? Or there is really no difference between the two? Thank you very much for your help.
PyRx uses autodock vina or autodock4 (up to you), so the final results are reported as binding energy (kcal/mol)
Both are basically binding free energies or Delta G. AutoDock 4 refers to it simply as binding energy and Vina refers to it as binding affinity. Both are same thing but the values are not comparable as they are calculated using different force fields. AutoDock 4 uses a semi-empirical force field and the details on the binding energy calculation can be found here: Article A Semiempirical Free Energy Force Field with Charge-Based Desolvation
. On the other hand, Vina uses a modified/weighted version (Article Software News and Update AutoDock Vina: Improving the speed ...
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