RFdiffusion3 (Foundry)

Basics

• Uploads mount at /inputs; write any results to /outputs for download.
• The service sets out_dir=/outputs and ckpt_path=rfd3_latest.ckpt for you; you do not need to include these.
• Your arguments are passed after rfd3 design inside the container.
• In general, prefer RF Diffusion (v1) unless you specifically want RFdiffusion3 and you’re confident with the Foundry input spec.
• RFdiffusion3 symmetry modes are not supported on SubSeq yet (use RF Diffusion (v1) for symmetry).

Example 1: unconditional monomer

Design a de novo monomer of length 120–130 residues with no structural input.

1. Create a JSON file under /inputs, for example /inputs/uncond_monomer.json:

{
  "uncond_monomer": {
    "length": "120-130"
  }
}

2. Submit a job with the following arguments (New Job → RFdiffusion3):

inputs=/inputs/uncond_monomer.json

RFdiffusion3 will sample one or more all-atom monomers in the requested length range and write PDB/CIF outputs under /outputs.

Example 2: simple protein binder

Design a small binder against a protein target using a minimal hotspot-based configuration.

1. Upload your target structure to /inputs, for example /inputs/target.pdb.
2. Create a JSON spec next to it, for example /inputs/protein_binder_simple.json:

{
  "simple_binder": {
    "dialect": 2,
    "input": "/inputs/target.pdb",
    "contig": "50-80,/0,A40-120",
    "infer_ori_strategy": "hotspots",
    "select_hotspots": {
      "A64": "CG,CD1",
      "A88": "CG,CD1"
    }
  }
}

3. Submit a job with:

inputs=/inputs/protein_binder_simple.json

In this setup:

• input is the target (antigen) structure you uploaded.
• contig requests a new binder segment of length 50–80 residues and treats residues A40–A120 of the target as the region of interest.
• infer_ori_strategy=hotspots and select_hotspots tell RFD3 to position the binder using atoms on residues A64 and A88 as hotspots.

Adjust the target residue window, hotspot residues/atoms, and binder length range to match your system.

Notes

• Multiple design specs can be placed in a single JSON file; each key is treated as an independent configuration.
• Standard Foundry examples for nucleic acid binders, small-molecule binders, and enzymes can be adapted by pointing paths into /inputs and keeping outputs in /outputs.
• For full input-spec details, see the RFdiffusion3 documentation in the Foundry repo: models/rfd3/docs/input.md.

Submit

Launch from New Job → RFdiffusion3. Keep all uploaded config and structure files under /inputs; outputs will appear under /outputs on completion.