ESMFold2 design — scFv CDRs + minibinders
Gradient-based binder design via ESMFold2 inversion. Pick a paper-validated target preset, choose minibinder or scFv mode, and get ranked designs with iPTM scores in one model pass.
What it is for
ESMFold2 design — scFv CDRs + minibinders runs on a dedicated GPU through the Ranomics tools hub. Pick the run size that fits your goal, submit your inputs, and read the ranked results on the job page.
Inputs
Each run uses a preset that sets the scale and scope:
- De novo minibinder (60-200 aa)
- Free 60-200 aa scaffold generated with an isoelectric-point filter (pI < 6) baked in. No framework constraints. Equivalent goal to RFdiffusion + ProteinMPNN but in one gradient pass through ESMFold2.
- scFv with framework-locked CDRs
- All six CDRs designed jointly on a locked humanized framework. Three frameworks available: trastuzumab, atezolizumab, ocankitug. The only catalog tool that designs paired heavy + light scFv CDRs end-to-end.
How to read the results
Where a tool reports them, the scores mean:
- ipTM
- Predicted confidence in the binder to target interface. Higher is better. Aim above roughly 0.7 on a tractable target.
- pLDDT
- Per-residue confidence in the predicted fold. Higher means the model is more sure of that part of the structure.
- i_pAE and pAE
- Predicted alignment error, at the interface (i_pAE) or across the whole structure (pAE). Lower is better.