AF3 hallucinations appear in 7 of 10 seeds for a non-cognate TCR:pMHC pair
quaidmorris · x · 2026-07-22
AF3 hallucination frequency differs between cognate and non-cognate pairs
The post argues that AlphaFold3 hallucinates for both binders and non-binders, but the frequency of those hallucinations is informative.
Using the CMV epitope NLVPMVATV and its M5K mutant as an example:
- misdocked structures appear in 7/10 seeds for the non-cognate complex,
- while the cognate complex shows them only rarely.
The image contrasts the two ensembles and illustrates how structural inconsistency can separate the two cases.
Related event: enFoldX Turns AlphaFold3 Noise into TCR Recognition Signals(11 posts)→
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