# HADDOCK Score vs PRODIGY binding affinity in the case of mutations

**URL:** <https://ask.bioexcel.eu/t/haddock-score-vs-prodigy-binding-affinity-in-the-case-of-mutations/4482>\
**Category:** HADDOCK\
**Created:** [September 3, 2023, 7:35pm UTC](https://ask.bioexcel.eu/t/haddock-score-vs-prodigy-binding-affinity-in-the-case-of-mutations/4482 "2023-09-03T19:35:11Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![deovine](https://avatars.discourse-cdn.com/v4/letter/d/bbce88/32.png) [@deovine](https://ask.bioexcel.eu/u/deovine)\
**Post date:** [September 3, 2023, 7:35pm UTC](https://ask.bioexcel.eu/t/haddock-score-vs-prodigy-binding-affinity-in-the-case-of-mutations/4482/1 "2023-09-03T19:35:11Z")

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The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [HADDOCK – Bonvin Lab](http://www.bonvinlab.org/software/haddock2.4)

If I were to choose one best mutation between two, mutation A has better HADDOCK Score but mutation B has better binding affinity obtained from PRODIGY, which aspect should I prioritize in choosing the best mutation?

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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 12, 2023, 8:01am UTC](https://ask.bioexcel.eu/t/haddock-score-vs-prodigy-binding-affinity-in-the-case-of-mutations/4482/2 "2023-12-12T08:01:14Z")

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None of the tools has been trained to predict ddG, which is what you are trying to do…

I would also try other tools like e.g.:

[https://biosig.lab.uq.edu.au/mcsm\_ppi2/](https://biosig.lab.uq.edu.au/mcsm_ppi2/)  
[https://biosig.lab.uq.edu.au/tools](https://biosig.lab.uq.edu.au/tools)  
[https://www.ibg.edu.tr/research-programs/groups/karaca-lab/](https://www.ibg.edu.tr/research-programs/groups/karaca-lab/)  
…

We also published iSee as ddG predictor:

- C. Geng, A. Vangone, G.E. Folkers, L.C. Xue and A.M.J.J. Bonvin. [iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations](https://doi.org//10.1002/prot.25630). _Proteins: Struc. Funct. & Bioinformatics_ _87_, 110-119 (2019).

and a review on the topic:

- C. Geng. Li J. Roel-Touris and A.M.J.J. Bonvin. [Finding the ∆∆G spot: Are predictors of binding affinity changes upon mutations in protein-protein interactions ready for it?](https://onlinelibrary.wiley.com/doi/full/10.1002/wcms.1410) _WIREs Computational Molecular Science_ _9_, e1410 (2019).