Protein ensemble prediction methods do not generate conformations that are amenable to PPI docking

Summary

Protein ensemble prediction methods do not generate conformations that can be used for PPI docking (1). This was even the case when the resulting structures were closer in RMSD than the alternative conformation (e.g., the apo unbound state normally being predicted).

See also

• Protein structure prediction methods are unable to predict the energetics of a conformational landscape unless explicitly trained for that purpose

1.

Stratiichuk R, Kyrylenko R, Koleiev I, Savchenko I, Voitsitskyi T, Husak V, et al. Sampling and Ranking of Protein Conformations Using Machine Learning Techniques Do Not Improve the Quality of Rigid Protein–Protein Docking. Journal of Chemical Information and Modeling. 2025;65(19):10167–79. Available from: https://doi.org/10.1021/acs.jcim.5c01765