Prodigy "Protein-Protein" or "Protein-LIG" for protein-peptide complexes


I have a set of protein-peptide complexes for which I want to predict binding affinity.

My questions are:

  1. Which tool should I use in the case of protein-peptide complexes (peptide < 30aa), the one for protein-protein or the one for protein-ligand?

  2. Did the traning of the protein-ligand model contain occurrences of peptides as small ligands?

Thank you!

Hi Sandra

None of the two has been benchmarked for peptides…

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