Getting different predicted pKa values compared to those stated in the paper.

[ndonyapour]

Hello, I'm trying to reproduce the pKa predictions for several structures in the OnionNet_Core_2016 test set, but the values I'm getting differ from those in the paper. Attached is a plot comparing the pKa values from the paper (x-axis) with the predicted values from our workflow (y-axis). Could you please provide details (share your code) on your workflow for structure preparation, running AutoDock-Vina, and selecting the optimal poses?

Thank you, Nazanin