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 | 0.8441 | 0.9003 | 0.905 | — | |
| binary | unconstrained | 2 | 0.7944 | 0.8663 | 0.882 | — | |
| binary | unconstrained | 3 | 0.8369 | 0.9307 | 0.873 | — | |
| binary | unconstrained | 4 | 0.8293 | 0.9107 | 0.872 | — | |
| binary | unconstrained | 5 | 0.8221 | 0.9039 | 0.892 | — | |
| ternary | unconstrained | 1 | 0.9298 | 0.9687 | 0.788 | -0.596 | |
| ternary | unconstrained | 2 | 0.8619 | 0.9449 | 0.795 | -0.564 | |
| ternary | unconstrained | 3 | 0.9090 | 0.9489 | 0.791 | -0.620 | |
| ternary | unconstrained | 4 | 0.7966 | 0.9163 | 0.811 | -0.504 | |
| ternary | unconstrained | 5 | 0.9277 | 0.9598 | 0.815 | -0.632 |
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.