RFdiffusion3

Overview

Protein binder design against a target structure and hotspot residues.
Unconditional all-atom monomer generation from a length range.
Cyclic, tetrahedral, octahedral, or icosahedral symmetric oligomer generation.

Modes

Mode	Input shape	When to use it
`binder_design` Binder Design Default	Uses one selected file/source when file parameters are present.	Design binders against a target structure using binder length and hotspot residues.
`unconditional_monomer` Unconditional Monomer	No uploaded input is required by the mode itself.	Generate de novo monomers from a requested length range.
`symmetric_unconditional` Symmetric Oligomer	No uploaded input is required by the mode itself.	Generate cyclic or polyhedral oligomers using the RFD3 symmetry sampler.

Canonical Job Configuration

These are the fields exposed by the default job configuration for rfdiffusion3. They are also returned by GET /api/v1/program/params?program=rfdiffusion3 and submitted as the params JSON object to POST /api/v1/job/submit.

Parameter	Type	Modes	What it does
`target_structure` Target Structure	Structure file	Binder Design	Choose the target structure from an upload, dataset, or previous job output. Required; Files: .pdb, .cif
`spec_name` Spec Name	Text	All modes	Optional key name for the generated RFD3 input spec.
`num_structures` Structures	Integer	All modes	How many structures to generate. Default: 10; Range: 1-10000
`output_format` Output Type	Text	All modes	Structure output type written after RFdiffusion3 finishes. Default: cif; Options: cif, pdb, cif.gz
`length` Length	Length or range	Unconditional Monomer	Length or length range for the generated monomer. Required; Range: 3-2000
`asu_length` ASU Length	Length or range	Symmetric Oligomer	Asymmetric-unit length or range. Total residues are capped near 2500, so the max updates from the selected symmetry. Required; Range: 3-1250
`symmetry_type` Symmetry Type	Text	Symmetric Oligomer	The job form supports cyclic plus T/O/I symmetry. Dihedral is intentionally omitted. Required; Default: Cyclic; Options: Cyclic, Tetrahedral, Octahedral, Icosahedral
`cyclic_order` Cyclic Copies	Integer	Symmetric Oligomer	Number of cyclic repeats. For example, 3 generates C3 symmetry. Required; Default: 3; Range: 2-60; Shown when symmetry_type is Cyclic
`binder_length` Binder Length	Length or range	Binder Design	Length or length range for the generated binder chain. Required; Range: 3-500
`hotspots` Hotspots	Residue selection	Binder Design	Residue-level hotspot selection; this avoids atom-name validation failures. Required

Advanced configuration fields

Parameter	Type	Modes	What it does
`target_segments` Target Segments	Residue selection	Binder Design	Full target chain segment(s) to keep in the binder-design context. This is auto-filled from the selected structure and hotspots. Required
`num_timesteps` Sampling Steps	Integer	All modes	mode default Range: 1-500
`step_scale` Step Scale	Number	All modes	mode default Range: 0.01-10
`dump_trajectories` Dump Trajectories	Yes/no	All modes	Trajectory dumps can make outputs much larger. Default: false

Outputs And Metrics

Generated all-atom structure files in CIF, PDB, or compressed CIF format.
Matching JSON metadata files and structure collections for downstream steps.
RFdiffusion3 outputs are generated candidates. Use downstream prediction, interface confidence, clash checks, and filtering to prioritize.

Common Examples

Binder design: target structure, binder length 70-100, hotspots A64,A88, 10 structures.
Unconditional monomer: length 120-130, 10 structures.
Symmetric oligomer: ASU length 40, cyclic order 3 or T/O/I symmetry, CIF output.

Example API params

{
  "mode": "binder_design",
  "target_structure": "target.pdb",
  "binder_length": "70-100",
  "hotspots": "A64,A88",
  "target_segments": "A1-180",
  "num_structures": 10,
  "output_format": "cif"
}

Caveats

Hotspot residue selection should be focused and must match the uploaded target numbering.
High-order symmetry can produce clashing samples; inspect and filter outputs.
PDB has chain/residue/atom-count limits; use CIF for large or many-chain designs.

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 direct RFdiffusion3 input specs and sampler overrides for specialized designs.
Use n_batches and diffusion_batch_size for design count when working at the direct-argument level.

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=rfdiffusion3 \
  -F 'params={"mode":"binder_design","target_structure":"target.pdb","binder_length":"70-100","hotspots":"A64,A88","num_structures":10,"output_format":"cif"}'