Res ipSAE adhuc loquuntur: What the directionality of predicted aligned error in cofolding models can tell us about scoring diverse molecular complexes
AlphaFold 3 (AF3) and Boltz-2 estimate confidence in predicted biomolecular complexes using the interface predicted template modeling (ipTM) score, which is derived from probability distributions of predicted aligned errors (PAEs) between molecular tokens. These errors are directional: the predicted position of tokens in one molecule is evaluated relative to coordinate frames defined by tokens in…
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