What does AlphaFold3 learn about antigen and nanobody docking, and what remains unsolved?

Antibody therapeutic development is a major focus in healthcare. To accelerate drug development, significant efforts have been directed towards the design and screening of antibodies for which high modeling accuracy is necessary. To probe AlphaFold3's (AF3) capabilities and limitations, we tested AF3's ability to capture the fine details and interplay between antibody structure prediction and antigen docking accuracy.