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 | 0.8751 | 0.9097 | 0.899 | — | |
| binary | unconstrained | 2 | 0.8558 | 0.9071 | 0.863 | — | |
| binary | unconstrained | 3 | 0.7948 | 0.9160 | 0.861 | — | |
| binary | unconstrained | 4 | 0.8252 | 0.8416 | 0.883 | — | |
| binary | unconstrained | 5 | 0.8691 | 0.9076 | 0.888 | — | |
| ternary | conditioned | 1 | 0.9135 | 0.9850 | 0.926 | -0.432 | |
| ternary | conditioned | 2 | 0.8839 | 0.9787 | 0.923 | -0.473 | |
| ternary | conditioned | 3 | 0.9043 | 0.9831 | 0.927 | -0.515 | |
| ternary | conditioned | 4 | 0.8980 | 0.9816 | 0.919 | -0.427 | |
| ternary | conditioned | 5 | 0.9140 | 0.9845 | 0.930 | -0.444 | |
| ternary | unconstrained | 1 | 0.9139 | 0.9848 | 0.929 | -0.207 | |
| ternary | unconstrained | 2 | 0.8856 | 0.9789 | 0.928 | -0.238 | |
| ternary | unconstrained | 3 | 0.8758 | 0.9746 | 0.900 | -0.262 | |
| ternary | unconstrained | 4 | 0.9004 | 0.9821 | 0.922 | -0.171 | |
| ternary | unconstrained | 5 | 0.9136 | 0.9846 | 0.930 | -0.166 |
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.