Structure-based methods outperform sequence-based methods on antigen-dependent antibody design

Summary

Structure-based methods such as inverse folding methods outperform sequence-based methods such as PLMs on the design of high-affinity antibodies (1). This is irrespective of whether the language model was trained on antibodies (AbLang) or generic proteins (ESM-1v).

Figures

Ref (1)

See also

• Structure-based methods outperform sequence-based methods on protein stability prediction of point mutants, but not full sequences

1.

Shanker VR, Bruun TUJ, Hie BL, Kim PS. Unsupervised evolution of protein and antibody complexes with a structure-informed language model. Science. 2024;385(6704):46–53. Available from: https://doi.org/10.1126/science.adk8946