TL;DR
A focused sequence-to-structure UI over per-model run endpoints.
Use it / Skip it
Use it when you already have a VHH or paired VH + VL sequences and only need the standalone antibody structure as a PDB.
Use when
You have an existing antibody sequence and need a quick structure for inspection or downstream review; choose ImmuneBuilder.
Don't use for
Do not use it for de novo antibody design (use RFantibody) or antibody-antigen complex assessment (use Interface).
Inputs
- Backend
- ImmuneBuilder for an existing VHH or VH + VL; Boltz-2 or AlphaFold only for deliberate multimer work.
- Sequence
- VHH in the primary field, or separate VH and VL fields for a paired antibody.
- Chain context
- ImmuneBuilder treats one sequence as Nanobody and VH + VL as Antibody.
Outputs
- PDB
- Returned or downloadable structure artifact.
- Job metadata
- job_id and status from the model run endpoint.
- Inline preview
- Rendered structure when the returned artifact is available in-page.
Walkthrough
1. Keep ImmuneBuilder selected for an existing VHH or VH + VL structure prediction
Keep ImmuneBuilder selected for an existing VHH or VH + VL structure prediction.
2. Paste a clean VHH sequence, or provide VH and VL in their separate fields
Paste a clean VHH sequence, or provide VH and VL in their separate fields.
3. Run the model endpoint and wait for result
Run the model endpoint and wait for result.
4. Download the PDB or inspect the inline structure
Download the PDB or inspect the inline structure.
Under the hood
- Wraps /api/v1/models/{key}/run.
- Multimer backends can take 10-30 minutes depending on configuration.
Worked example
Pitfalls
- A folded binder alone does not show antigen binding.
- Wrong backend choice can return poor or irrelevant structures.
- Do not submit a fused scFv as a Nanobody; this focused ImmuneBuilder form expects VHH or separate VH and VL sequences.