Learn/Redesign a sequence
Fold them back
A redesign is only a redesign if the new sequence folds back into the structure it was written for. ESMFold refolds the designed chain from its sequence alone in about a minute; its per-residue pLDDT says how confidently each residue is placed, and superposing the refold on the input gives the Cα RMSD, how far the backbone moved. The partner chain is not refolded: whether the new chain still binds is a second question, for a co-folding model.
The designs, refolded
| Model | Design | Mean pLDDT |
|---|---|---|
| ProteinMPNN | design 1 | 77.3 |
| ProteinMPNN | design 2 | 76.9 |
| ProteinMPNN | design 3 | 77.4 |
| ProteinMPNN | design 4 | 76.9 |
| PottsMPNN | design 2 | 79.3 |
| PottsMPNN | design 3 | 78.1 |
| PottsMPNN | design 4 | 78.3 |
| PottsMPNN | design 1 | 77.6 |
| ESM-IF1 | design 1 | 77.2 |
| ESM-IF1 | design 2 | 75.7 |
| ESM-IF1 | design 3 | 77.6 |
| ESM-IF1 | design 4 | 79.4 |
| Proton-PottsMPNN | design 1 | 77.5 |
| Proton-PottsMPNN | design 2 | 76.6 |
| Proton-PottsMPNN | design 3 | 51.4 |
| Proton-PottsMPNN | design 4 | 54.8 |
In the lab, Fold the designs on the Review step sends one ESMFold job per design and fills the pLDDT column as they land; picking a design shows its refold in pLDDT in the instrument, and Redesign from this one makes that refold the structure of the next round. pLDDT reads on the same four steps as everywhere on the site: 90 and above very high confidence, 70 to 89 confident, 50 to 69 low, below 50 very low.
Read more: Lin et al. 2023, ESMFold · Phi docs: confidence