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

**URL:** <https://ask.bioexcel.eu/t/prodigy-protein-protein-or-protein-lig-for-protein-peptide-complexes/3358>\
**Category:** PRODIGY\
**Created:** [November 30, 2021, 11:44am UTC](https://ask.bioexcel.eu/t/prodigy-protein-protein-or-protein-lig-for-protein-peptide-complexes/3358 "2021-11-30T11:44:52Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![sandra.romero](https://avatars.discourse-cdn.com/v4/letter/s/2acd7d/32.png) [@sandra.romero](https://ask.bioexcel.eu/u/sandra.romero)\
**Post date:** [November 30, 2021, 11:44am UTC](https://ask.bioexcel.eu/t/prodigy-protein-protein-or-protein-lig-for-protein-peptide-complexes/3358/1 "2021-11-30T11:44:52Z")

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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!

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [December 6, 2021, 9:46am UTC](https://ask.bioexcel.eu/t/prodigy-protein-protein-or-protein-lig-for-protein-peptide-complexes/3358/2 "2021-12-06T09:46:44Z")

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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](https://pubs.acs.org/doi/abs/10.1021/ci4005332) _J. Chem. Info. Model._ _54_, 826-836 (2014).