Summary
AlphaFold3 antibody-antigen confidence is biased by antigen size (1). Larger antigens lead to broader PAE distributions, presumably because there are more ways to be very wrong in larger antigens than smaller antigens.
Figures
Ref (1)
See also
- AlphaFold3 ipTM can distinguish between antibody binders and nonbinders
- ipTM is sensitive to construct length even when predicted interfaces are unchanged
- Correct antibody-antigen prediction in AF3 and related models is partially determined by training set similarity
1.
Solanki A, Maurya NS, Ramlakhan M, Li R, Chen W, Wu Z, et al. A Structural Antibody Benchmark of AlphaFold3 reveals Hallucinated Epitopes and a Bias for Orderness. bioRxiv. 2026; Available from: https://doi.org/10.64898/2026.07.30.741792