Paratope losses are required to enforce CDR-mediated antigen binding during de novo antibody design by hallucination

Summary

Paratope losses are required to enforce CDR-mediated antigen binding during de novo antibody design by hallucination (1).

Details

The exact paratope loss implementation:

$${\mathcal{L}}_{\text{paratope}}=\frac{{\mathcal{L}}_{\text{CDR}}}{{\mathcal{L}}_{\text{framework}}-\lambda }$$

where ${\mathcal{L}}_{\text{CDR}}$ and ${\mathcal{L}}_{\text{framework}}$ decrease as the respective regions gain more contacts with the antigen, and $\lambda$ is a user-defined parameter.

Figures

Ref (1)

See also

• Secondary structure losses are required to enforce CDR loopiness during de novo antibody design by hallucination

1.

Mille-Fragoso LS, Driscoll CL, Wang JN, Dai H, Widatalla T, Zhang JL, et al. Efficient generation of epitope-targeted de novo antibodies with Germinal. openRxiv; 2025. Available from: https://doi.org/10.1101/2025.09.19.677421