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 | 0.7961 | 0.9048 | 0.894 | — | |
| binary | unconstrained | 2 | 0.7980 | 0.9035 | 0.893 | — | |
| binary | unconstrained | 3 | 0.8713 | 0.8992 | 0.894 | — | |
| binary | unconstrained | 4 | 0.7232 | 0.8935 | 0.890 | — | |
| binary | unconstrained | 5 | 0.8415 | 0.9078 | 0.893 | — | |
| ternary | conditioned | 1 | 0.9135 | 0.9412 | 0.907 | 1.159 | |
| ternary | conditioned | 2 | 0.9172 | 0.9422 | 0.905 | 1.221 | |
| ternary | conditioned | 3 | 0.9124 | 0.9400 | 0.905 | 1.225 | |
| ternary | conditioned | 4 | 0.9081 | 0.9341 | 0.905 | 1.210 | |
| ternary | conditioned | 5 | 0.9179 | 0.9401 | 0.907 | 1.146 | |
| ternary | unconstrained | 1 | 0.9145 | 0.9407 | 0.907 | 1.398 | |
| ternary | unconstrained | 2 | 0.9202 | 0.9440 | 0.905 | 1.341 | |
| ternary | unconstrained | 3 | 0.9205 | 0.9390 | 0.904 | 1.324 |
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.