Toward Chemical Interpretability of AI-Predicted Poses
Cofolding models like AlphaFold3, OpenFold3, Boltz-2, and Chai-1 can generate protein–ligand complexes that look convincing but often break basic chemical rules. In this post, we describe how post-processing steps such as restoring bond types, hydrogens, and realistic geometry can make these AI-predicted poses chemically interpretable and ready for downstream modeling.