The structures of nanobodies with kinked CDR3 loops are more difficult to predict in complex with their antigen

Summary

The structures of nanobodies with kinked CDR3 loops are more difficult to predict in complex with their antigen (1). The failure rate (DockQ < 0.23) for nanobody/antigen complex prediction when the CDR3 was kinked was nearly 75% with AlphaFold3 and even higher with AlphaFold2.

Figures

Ref (1)

See also

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

1.

Eshak F, Goupil-Lamy A. Advancements in Nanobody Epitope Prediction: A Comparative Study of AlphaFold2Multimer vs AlphaFold3. Journal of Chemical Information and Modeling. 2025;65(4):1782–97. Available from: https://doi.org/10.1021/acs.jcim.4c01877