Summary
Antibody-antigen complex prediction by diffusion-based structure prediction methods is data-limited (1). This is not true of other poor-performing tasks, such as small molecule docking. This was observed using a version of Protenix trained on four additional years of public data.
Figures
| Model | Ab-Ag DQ SR(%) | Ab-Ag lDDT |
|---|---|---|
| Chai-1 | 21.12 | 0.1972 |
| Boltz-1 | 12.02 | 0.1577 |
| Boltz-2 | 19.20 | 0.1606 |
| Protenix-v0.5.0 | 15.58 | 0.1713 |
| Protenix-v1 | 24.11 | 0.2488 |
| Protenix-v1-20250630 | 39.49 | 0.3574 |
Ref (1)
1.
Zhang Y, Gong C, Zhang H, Ma W, Liu Z, Chen X, et al. Protenix-v1: Toward High-Accuracy Open-Source Biomolecular Structure Prediction. openRxiv; 2026. Available from: https://doi.org/10.64898/2026.02.05.703733