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

[sandra.romero]

Hi,

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!

[amjjbonvin]

Hi Sandra

None of the two has been benchmarked for peptides…

You might also check:

• P.L. Kastritis, J.P.G.L.M. Rodrigues and A.M.J.J. Bonvin HADDOCK2P2I: A robust biophysical model for predicting the binding affinity of protein-protein interaction inhibitors J. Chem. Info. Model. 54, 826-836 (2014).