HADDOCK score vs. Prodigy Binding energy?

1

Hello,

I have several representative conformations for a protein-peptide complex calculated with HADDOCK 2.4. I have the HADDOCK score and also the Prodigy Binding Energy for the same complex. If I want to select the best representative conformation, which parameter should I trust more, the HADDOCK score or the Prodigy Binding Energy?

Best Regards
D

2

I would trust more the HADDOCK score.

Also PRODIGY has not been trained on protein-peptide complexes.