Pose
The predicted ternary in 3D. Receptor as cartoon, peptide as a tube coloured by per-residue pLDDT, ligand as ball-and-stick. Controls reuse BINMAN's viewer idiom.
Presentation is BINMAN's, unchanged: the AlphaFold four-band pLDDT scale, a translucent gaussian surface over the polymer, and the ligand as sticks inside an emissive shell so it reads through the surface. The per-seed geometry below is the text alternative: every number the viewer can show is in the table.
Per-seed geometry
| Job | Complex | Conditioning | Seed | ipTM (receptor-peptide) | ipTM (global) | pLDDT | Affinity |
|---|---|---|---|---|---|---|---|
| binary | unconstrained | 1 | 0.8855 | 0.9586 | 0.900 | — | |
| binary | unconstrained | 2 | 0.8340 | 0.9442 | 0.896 | — | |
| binary | unconstrained | 3 | 0.8627 | 0.9519 | 0.897 | — | |
| binary | unconstrained | 4 | 0.8429 | 0.9521 | 0.900 | — | |
| binary | unconstrained | 5 | 0.8313 | 0.9396 | 0.904 | — | |
| ternary | conditioned | 1 | 0.8950 | 0.9477 | 0.885 | -0.780 | |
| ternary | conditioned | 2 | 0.8626 | 0.9503 | 0.894 | -0.975 | |
| ternary | conditioned | 3 | 0.8161 | 0.9458 | 0.860 | -0.645 | |
| ternary | conditioned | 4 | 0.7308 | 0.9449 | 0.875 | -0.960 | |
| ternary | conditioned | 5 | 0.7883 | 0.9458 | 0.886 | -0.717 | |
| ternary | unconstrained | 1 | 0.9092 | 0.9470 | 0.873 | -0.785 | |
| ternary | unconstrained | 2 | 0.8863 | 0.9460 | 0.862 | -0.786 | |
| ternary | unconstrained | 3 | 0.8695 | 0.9521 | 0.855 | -0.488 | |
| ternary | unconstrained | 4 | 0.7937 | 0.9421 | 0.875 | -0.764 | |
| ternary | unconstrained | 5 | 0.7780 | 0.9454 | 0.866 | -0.783 |
Affinity is recorded for the small-molecule chain only and is never a ranking key (spec 4.7). There is no protein-protein affinity path in Boltz-2, so no peptide affinity is reported anywhere in this application.