New preprint uses AlphaFold3 ensembles to predict TCR–pMHC binding
quaidmorris · x · 2026-07-25
A recent preprint introduces enFoldX, a structure-ensemble method for predicting whether a TCR and a peptide-MHC pair are cognate binders.
- Instead of trusting a single AlphaFold3 co-folded structure, the method featurizes many sampled complex structures.
- The key insight is that AF3 can produce plausible-looking false positives for non-cognate pairs, especially when sequences differ only subtly.
- enFoldX turns that weakness into a signal by analyzing how confidence and interface geometry vary across the ensemble.
- The approach focuses on features at the binding interface rather than on one “best” predicted structure.
This is a concrete AI-for-biology method paper rather than a product announcement.
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