Summary
Different AlphaFold3 clones have differently calibrated confidence heads. AF3-family and open-source clone confidence heads differ in calibration and binder-filtering behavior, affecting their suitability for antibody-antigen docking and design workflows (1,2).
Figures
Figure from (1)
Figure from (2)
See also
- The confidence metrics of AlphaFold2 are better calibrated than those of AlphaFold3
- AlphaFold3 ipTM can distinguish between antibody binders and nonbinders
- Structure prediction uncertainty metrics as energy functions
1.
Jing B, Bafna M, Diaz D, Klivans A, Berger B. Promera: a unified model for biomolecular structure prediction, filtering, and design. openRxiv; 2026. Available from: https://doi.org/10.64898/2026.06.07.729267
2.
Smorodina E, Ali M, Kropivšek Brumat K, Salicari L, Miklavc S, Kappassov A, et al. Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores. openRxiv; 2026. Available from: https://doi.org/10.64898/2026.03.02.709004