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 | 0.7222 | 0.8796 | 0.832 | — | |
| binary | unconstrained | 2 | 0.7932 | 0.9212 | 0.829 | — | |
| binary | unconstrained | 3 | 0.7912 | 0.8763 | 0.851 | — | |
| binary | unconstrained | 4 | 0.8232 | 0.9283 | 0.816 | — | |
| binary | unconstrained | 5 | 0.6070 | 0.7567 | 0.848 | — | |
| ternary | conditioned | 1 | 0.9336 | 0.9660 | 0.958 | -0.524 | |
| ternary | conditioned | 2 | 0.9277 | 0.9642 | 0.958 | -0.485 | |
| ternary | conditioned | 3 | 0.9293 | 0.9664 | 0.958 | -0.521 | |
| ternary | conditioned | 4 | 0.9259 | 0.9673 | 0.953 | -0.491 | |
| ternary | conditioned | 5 | 0.9248 | 0.9621 | 0.958 | -0.521 | |
| ternary | unconstrained | 1 | 0.9324 | 0.9654 | 0.958 | -0.291 | |
| ternary | unconstrained | 2 | 0.9283 | 0.9637 | 0.959 | -0.247 | |
| ternary | unconstrained | 3 | 0.9265 | 0.9640 | 0.958 | -0.293 | |
| ternary | unconstrained | 4 | 0.9226 | 0.9656 | 0.953 | -0.258 | |
| ternary | unconstrained | 5 | 0.9229 | 0.9609 | 0.959 | -0.266 |
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.