TL;DR
Structure-based antibody/nanobody design runner with framework presets, hotspot input, gates, job history, and artifact downloads.
Use it / Skip it
RFantibody is the specialized structure-generation path when you need a configured GPU runner and explicit design gates.
Use when
You have a target PDB, hotspot residues, and want RFdiffusion-Ab/ProteinMPNN/RF2-Ab style design artifacts.
Don't use for
Do not use it when the GPU runner is not configured; the page will block submission.
Inputs
- Target PDB
- Uploaded PDB structure.
- Hotspots
- Residue tokens that define the binding patch.
- Framework preset
- Runner-provided framework options.
- Gates
- pAE, RMSD, ddG and related thresholds shown from runner status.
Outputs
- Run or job record
- A persisted job with status, timestamps, inputs, and enough context to reopen it later.
- Artifacts
- CSV, JSON, PDB, or report files depending on the module.
- Decision signal
- A shortlist, score, verdict, or review note that supports the next wet-lab or design step.
Walkthrough
1. Wait for runner status
Wait for runner status. Submission is enabled only when configured.
2. Upload target PDB and set hotspots
Upload target PDB and set hotspots.
3. Choose framework preset and number of designs within runner limits
Choose framework preset and number of designs within runner limits.
4. Run RFantibody and monitor recent jobs
Run RFantibody and monitor recent jobs.
5. Download artifacts when a job reaches done
Download artifacts when a job reaches done.
Under the hood
- Uses RFantibody API helpers for runner status, submit, job polling, and artifact URLs.
- The configured GPU runner controls max designs, framework presets, and default gates.
Worked example
Pitfalls
- No configured runner means no real run.
- Hotspot residue formatting matters; bad hotspots produce bad designs.
- Do not scale design count before a small sanity run succeeds.