Physical Implausibility of Carbohydrate Ligands in Results of Deep Learning-Based Cofolding Methods

Stereochemistry violations in AlphaFold 3 models are more prevalent than currently appreciated. Analysis of 900 carbohydrate ligands revealed that 85.8% have errors, mainly in chirality but also including bond conversions (15.2%), planar ring distortions (3.9%), aromatic ring formations (2.5%), and improper structural configurations (0.9%). Boltz-1x reduced most violations dramatically but increased improper configurations to 22.1%, notably in N-acetyl-α-neuraminic acid. The BondedAtomPairs protocol reduced stereochemical issues but lost the reducing-end anomeric oxygen, highlighting ongoing challenges in accurate carbohydrate modeling.