Protein Design · Binder design

RFdiffusion API

Generate protein backbones unconditionally, around a motif, or against a target.

Runs the official RFdiffusion inference script. Custom Contigs exposes the raw contig map directly; the other tasks build one for you from a target/binder/motif description.

Web form Source code ↗

Submit POST /api/rfdiffusion/

Queues a run and returns 202 with the job.

Schema GET /api/rfdiffusion/

Returns this tool's metadata and the fields below, as JSON.

Tasks

Pick a mode with `task`

Fields belonging to another task are ignored, so send only the ones for the task you chose.

task	Mode
`contigs` default	Custom contigs
`binder_design`	Binder design
`binder_redesign`	Binder redesign
`motif_scaffolding`	Motif scaffolding
`partial_diffusion`	Partial diffusion
`fold_conditioning`	Fold conditioning
`symmetric_oligomer`	Symmetric oligomer
`symmetric_motif`	Symmetric motif scaffolding

Request body

Fields

The same names the web form posts. See the field type table for what each kind means over HTTP.

Name	Type	Required	Default	Description
`job_name`	string text	no	`rfdiffusion-demo`	Job name
`num_designs`	number number	no	`2`	Backbone designs minimum 1, maximum 1000.
`diffusion_steps`	number number	no	`50`	Diffusion steps minimum 15, maximum 200.
`contigs` contigs	string text	yes	`150-150`	Contig map RFdiffusion contig string without the brackets. For example 150-150 for an unconditional monomer, 5-15/A10-25/30-40 to scaffold a motif, or B1-100/0 100-100 for a binder.
`input_pdb` contigs	string file	no	`—`	Input PDB (optional) Required by any contig that references chains of a structure. file types .pdb,.ent.
`hotspot_chain` contigs	string text	no	`—`	Hotspot chain (optional)
`hotspots` contigs	string text	no	`—`	Hotspot residues (optional) Comma- or space-separated residue numbers on hotspot_chain, e.g. 100,101,102.
`binder_design_input_pdb` binder_design	string file	yes	`HEADER PASTE A TARGET STRUCTURE PDB HERE`	Target PDB file types .pdb,.ent.
`target_chains` binder_design	string text	yes	`A`	Target chains Comma-separated chain IDs from the target PDB to keep as context.
`binder_length` binder_design	string text	yes	`70-100`	Binder length range e.g. 70-100.
`binder_hotspots` binder_design	string textarea	no	`—`	Target hotspots (optional) One "chain: residues" per line, e.g. "A: 20 21 23".
`binder_redesign_input_pdb` binder_redesign	string file	yes	`HEADER PASTE A TARGET-BINDER COMPLEX PDB HERE`	Target-binder complex PDB file types .pdb,.ent.
`redesign_hotspot_chain` binder_redesign	string text	no	`—`	Hotspot chain (optional)
`redesign_hotspots` binder_redesign	string text	no	`—`	Hotspot residues (optional) Comma- or space-separated residue numbers.
`binder_chain` binder_redesign	string text	yes	`B`	Binder chain
`designed_residues` binder_redesign	string text	yes	`26-32,52-57,99-110`	Designed residues Comma-separated ranges on binder_chain to regenerate; everything else on it stays fixed.
`designed_lengths` binder_redesign	string text	no	`—`	Designed lengths (optional) One length range per designed_residues range, e.g. 5-9,3-8,10-25. Blank keeps each span's original length.
`motif_input_pdb` motif_scaffolding	string file	yes	`HEADER PASTE A STRUCTURE CONTAINING THE MOTIF HERE`	Motif source PDB file types .pdb,.ent.
`interface_chain` motif_scaffolding	string text	yes	`A`	Motif chain
`interface_residues` motif_scaffolding	string text	yes	`30-40, 60-70`	Motif residues Comma-separated ranges of the motif to preserve.
`motif_designed_lengths` motif_scaffolding	string text	no	`—`	Scaffold gap lengths (optional) One range per gap (one more than the number of motif ranges), e.g. 10-40,10-40,10-40. Blank defaults every gap to 10-40.
`partial_input_pdb` partial_diffusion	string file	yes	`HEADER PASTE A STARTING STRUCTURE PDB HERE`	Starting structure PDB file types .pdb,.ent.
`designed_chain` partial_diffusion	string text	yes	`A`	Chain to partially diffuse
`diffused_residues` partial_diffusion	string text	yes	`1-79`	Diffused residues Comma-separated ranges on designed_chain to noise; other residues (and other chains) stay fixed.
`provide_seq` partial_diffusion	string text	no	`—`	Keep sequence fixed at (optional) Comma-separated ranges, in designed_chain's own residue numbering, to hold sequence identity constant even while noised.
`partial_t` partial_diffusion	number number	no	`20`	Partial noising steps minimum 1, maximum 199.
`fold_conditioning_target_file` fold_conditioning	string file	yes	`HEADER PASTE A TARGET STRUCTURE PDB HERE`	Target PDB file types .pdb,.ent.
`fold_conditioning_binder_file` fold_conditioning	string file	yes	`HEADER PASTE A STRUCTURE WITH THE DESIRED BINDER FOLD HERE`	Desired binder fold PDB A structure whose secondary-structure/block-adjacency pattern the new binder should follow. file types .pdb,.ent.
`fold_hotspot_chain` fold_conditioning	string text	no	`—`	Hotspot chain (optional)
`fold_hotspots` fold_conditioning	string text	no	`—`	Hotspot residues (optional)
`symmetry_type` symmetric_oligomer	string text	yes	`C4`	Symmetry e.g. C2, C4, C6, D2, tetrahedral, octahedral, icosahedral.
`oligomer_length` symmetric_oligomer	number number	no	`480`	Total oligomer length Divided evenly across the symmetric copies by RFdiffusion. minimum 10, maximum 10000.
`oligomer_use_contacts` symmetric_oligomer	boolean checkbox	no	`true`	Guide with an inter/intra-chain contact potential
`symmetric_motif_input_pdb` symmetric_motif	string file	yes	`HEADER PASTE A STRUCTURE WITH SYMMETRIC MOTIF COPIES HERE`	Structure containing the symmetric motif copies file types .pdb,.ent.
`motif_symmetry_type` symmetric_motif	string text	yes	`C4`	Symmetry
`motif_residues` symmetric_motif	string text	yes	`A2-4, A7-9, A12-14, A17-19`	Motif copies Comma-separated per-copy residue ranges, one per symmetric unit.
`scaffold_length_before` symmetric_motif	number number	no	`50`	Scaffold residues before each copy minimum 0, maximum 500.
`scaffold_length_after` symmetric_motif	number number	no	`50`	Scaffold residues after each copy minimum 0, maximum 500.
`motif_use_contacts` symmetric_motif	boolean checkbox	no	`true`	Guide with an inter/intra-chain contact potential
`checkpoint`	string select	no	`—`	Model checkpoint override (optional) One of: `(empty)`, `active_site`, `complex_base`, `complex_fold_base`, `inpaint_seq`, `inpaint_seq_fold`, `base_epoch8`.
`noise_scale_ca`	number number	no	`1`	CA noise scale minimum 0, maximum 2, step 0.05.
`noise_scale_frame`	number number	no	`1`	Frame noise scale minimum 0, maximum 2, step 0.05.
`potentials`	string text	no	`—`	Custom guiding potential (optional) Raw potential spec, e.g. "type:substrate_contacts,s:1,r_0:8,rep_r_0:5.0,rep_s:2,rep_r_min:1".
`substrate`	string text	no	`—`	Substrate CCD code (optional) Only used with a substrate_contacts potential, e.g. LLK.
`guide_scale`	number number	no	`10`	Guide scale minimum 0, maximum 50.
`guide_decay`	string select	no	`constant`	Guide decay One of: `constant`, `linear`, `quadratic`.

Example

A request that runs

These are the defaults, exactly as the web form would post them.

curl -X POST https://www.athanortools.com/api/rfdiffusion/ \
  -H 'Content-Type: application/json' \
  -d '{
  "task": "contigs",
  "job_name": "rfdiffusion-demo",
  "num_designs": 2,
  "diffusion_steps": 50,
  "contigs": "150-150",
  "input_pdb": "",
  "hotspot_chain": "",
  "hotspots": "",
  "checkpoint": "",
  "noise_scale_ca": 1,
  "noise_scale_frame": 1,
  "potentials": "",
  "substrate": "",
  "guide_scale": 10,
  "guide_decay": "constant"
}'

The reply is 202 with a queued job; poll its status_url until status is succeeded or failed. See the quick start for the whole exchange.

Responses

What comes back

status	Meaning
`queued`	Accepted, waiting for the jobs ahead of it. `position` counts how many those are.
`running`	The tool is executing now.
`succeeded`	Finished; `result` holds the tool's output and `license` the terms it came under.
`failed`	Finished; `error` holds a code and a message.

Errors

code	Meaning
`invalid_input`	The client supplied invalid or incomplete input.
`tool_unavailable`	The requested third-party dependency is not available on this host.
`execution_failed`	A configured third-party process exited unsuccessfully.
`internal_error`	An adapter failed in a way it does not describe. The detail is in the server log, not the response.
`not_found`	No job has that id. Finished jobs are dropped eventually.