Correct CDRH3 prediction is necessary but insufficient for correct Ab-Ag docking

Summary

Correct prediction of CDRH3 is necessary but insufficient for correct antibody-antigen docking (1,2). Improving CDRH3 prediction by providing templates can lead to improved docking prediction (3).

Figures

Ref (1)

Ref (2)

Ref (3)

See also

• Antibody-antigen binding modes are not necessarily defined by induced fit
• The structures of nanobodies with kinked CDR3 loops are more difficult to predict in complex with their antigen
• Correct protomer structure prediction is necessary but insufficient for accurate protein-protein docking

1.

Yin R, Pierce BG. Evaluation of AlphaFold antibody–antigen modeling with implications for improving predictive accuracy. Protein Science. 2023;33(1). Available from: https://doi.org/10.1002/pro.4865

2.

Hitawala FN, Gray JJ. What does AlphaFold3 learn about antigen and nanobody docking, and what remains unsolved?. openRxiv; 2024. Available from: https://doi.org/10.1101/2024.09.21.614257

3.

Li S, Mu Z, Yan C. Dissecting the Black Box of AlphaFold in Protein–Protein Complex Assembly. openRxiv; 2026. Available from: https://doi.org/10.64898/2026.04.03.716280