HADDOCK Score vs PRODIGY binding affinity in the case of mutations

[deovine]

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

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?

[amjjbonvin]

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/tools
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. 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? WIREs Computational Molecular Science 9, e1410 (2019).