RF Diffusion

Overview

De novo monomer backbone generation.
Symmetric oligomer design.
Binder design against a target surface.
Motif scaffolding and partial diffusion around existing structures.

Modes

Mode	Input shape	When to use it
`unconditional` Unconditional Default	No uploaded input is required by the mode itself.	Generate de novo monomer or symmetric oligomer backbones from a requested length range.
`binder_design` Binder Design	Uses one selected file/source when file parameters are present.	Design binders against a target structure with target residue context and hotspot residues.
`motif_scaffolding` Motif Scaffolding	Uses one selected file/source when file parameters are present.	Build new backbone around one or more fixed motif segments from an input structure.
`partial_diffusion` Partial Diffusion	Uses one selected file/source when file parameters are present.	Generate diversity around an existing backbone by noising and denoising a supplied structure.

Canonical Job Configuration

These are the fields exposed by the default job configuration for rfdiffusion. They are also returned by GET /api/v1/program/params?program=rfdiffusion and submitted as the params JSON object to POST /api/v1/job/submit.

Parameter	Type	Modes	What it does
`num_structures` Structures	Integer	All modes	How many structures to generate. Default: 3; Range: 1-100
`length` Backbone Length	Length or range	Unconditional	Length or length range for generated monomers, or per protomer when symmetry is enabled. Required
`target_structure` Target Structure	Structure file	Binder Design	Choose a PDB target from an upload, dataset, or previous job output. Required; Files: .pdb
`target_segment` Target Segment	Residue selection	Binder Design	Residues from the target to include as context, such as A1-150. Required
`binder_length` Binder Length	Length or range	Binder Design	Length or length range for the generated binder chain. Required
`hotspots` Hotspots	Residue selection	Binder Design	Target residues to bias the interface toward. Use comma-separated chain/residue IDs. Required
`motif_structure` Motif Structure	Structure file	Motif Scaffolding	Choose a PDB containing the motif residues to preserve. Required; Files: .pdb
`motif_segments` Motif Segments	Residue selection	Motif Scaffolding	Residues to preserve from the motif structure. Multiple segments can be comma- or slash-separated. Required
`n_flank_length` N-Flank Length	Length or range	Motif Scaffolding	Generated residues before the motif. Default: 10-40
`c_flank_length` C-Flank Length	Length or range	Motif Scaffolding	Generated residues after the motif. Default: 10-40
`input_structure` Input Structure	Structure file	Partial Diffusion	Choose the starting PDB to diversify. Required; Files: .pdb
`structure_length` Structure Length	Integer	Partial Diffusion	Total residue count in the input structure. For whole-structure partial diffusion this must match the PDB length. Required; Range: 1-2000
`partial_noise_steps` Noise Steps	Integer	Partial Diffusion	How far to noise the input before denoising. Lower values stay closer to the starting backbone. Default: 10; Range: 1-49
`symmetry_type` Symmetry Type	Text	Unconditional	RFdiffusion v1 supports cyclic, dihedral, and tetrahedral symmetric oligomers. Default: None; Options: None, Cyclic, Dihedral, Tetrahedral
`symmetry_order` Symmetry Order	Integer	Unconditional	Order for cyclic or dihedral symmetry. For example, Cyclic order 3 generates C3. Default: 3; Range: 2-60; Shown when symmetry_type is one of Cyclic, Dihedral

Advanced configuration fields

Parameter	Type	Modes	What it does
`sampling_steps` Sampling Steps	Integer	All modes	Diffusion trajectory length. Lower values are faster; 50 is the RFdiffusion v1 default. Default: 50; Range: 15-200
`binder_diversity` Binder Diversity	Text	Binder Design	Focused reduces sampling noise for tighter binder interfaces; Diverse keeps more RFdiffusion default noise. Default: Focused; Options: Focused, Balanced, Diverse
`mask_motif_sequence` Mask Motif Sequence	Yes/no	Motif Scaffolding	Allow selected motif residues to be redesigned while preserving their backbone positions. Default: false
`sequence_mask_segments` Sequence Mask Segments	Residue selection	Motif Scaffolding	Motif residues whose sequence identity should be hidden from RFdiffusion. Shown when mask_motif_sequence is true
`small_motif_model` Small Motif Model	Yes/no	Motif Scaffolding	Use the RFdiffusion active-site checkpoint for very small functional motifs. Default: false
`use_oligomer_contacts` Promote Chain Contacts	Yes/no	Unconditional	Use RFdiffusion's oligomer contact potential to encourage intra- and inter-chain contacts. Default: true; Shown when symmetry_type is one of Cyclic, Dihedral, Tetrahedral

Outputs And Metrics

Backbone PDBs and metadata sidecars.
Optional trajectories when requested.
Raw RFdiffusion outputs are backbone proposals. Downstream sequence design, structure prediction, RMSD checks, motif RMSD, and interface confidence are the usual triage steps.

Common Examples

Unconditional monomer: length 90-120, 8 structures.
C3 symmetric oligomer: length 80-100, cyclic symmetry order 3.
Binder design: target PDB, target segment A1-180, hotspots A42,A65,A91, binder length 70-100.
Motif scaffolding: motif structure, motif residues, N/C flank ranges, and small-motif model if appropriate.

Example API params

{
  "mode": "binder_design",
  "target_structure": "target.pdb",
  "target_segment": "A1-180",
  "binder_length": "70-100",
  "hotspots": "A42,A65,A91",
  "num_structures": 12
}

Caveats

Hotspots bias interfaces but do not guarantee binding.
Motif and hotspot residue numbering must match the uploaded PDB exactly.
Always validate with sequence design, independent prediction, biophysical sanity checks, and experiments.

Advanced Submit

Advanced submit is still available for direct program arguments through POST /api/v1/job/submit-advanced. Prefer canonical configuration unless you need exact low-level arguments or are reproducing a known command line.

Advanced submit exposes RFdiffusion contig strings, symmetry flags, motif settings, partial diffusion options, and sampling controls.
Use canonical configuration for common monomer, binder, motif, and partial diffusion modes.

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=rfdiffusion \
  -F 'params={"mode":"binder_design","target_structure":"target.pdb","target_segment":"A1-180","binder_length":"70-100","hotspots":"A42,A65,A91","num_structures":12}'