Structure prediction · Protein Design

OpenDDE API

Run a protein, DNA/RNA, or ligand co-folding prediction.

Predict protein structure from nucleic acid or amino acid sequence. Predict the structure of ligands, nucleic acids, and ions, or complexes of these molecules. This is a relatively new, but very accurate model.

Web form Documentation ↗ Home page ↗ Source code ↗

Submit POST /api/opendde/

Queues a run and returns 202 with the job.

Schema GET /api/opendde/

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
`sequence` default	Sequence
`list`	Chain list
`molecules`	Molecules (JSON)

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	`opendde-demo`	Job name
`sequence_molecules` sequence	string (JSON array) molecule_builder	yes	`[{"type": "protein", "sequence": "ACDEFGHIK", "cyclic": false, "modifications": []}]`	Molecules Add one box per chain: Protein, Ligand, DNA, or RNA. Ligands take a SMILES string or a CCD_ code (e.g. CCD_ATP). A modification applies a CCD residue code at a given position; "Cyclic" bonds the chain's first and last residue. One of: `protein`, `ligand`, `dna`, `rna`. A JSON array, sent as a string. See molecule entries.
`proteins` list	string textarea	yes	`ACDEFGHIK`	Protein chains One protein chain sequence per line.
`dnas` list	string textarea	no	`—`	DNA chains (optional) One DNA chain sequence per line.
`rnas` list	string textarea	no	`—`	RNA chains (optional) One RNA chain sequence per line.
`molecules` molecules	string textarea	yes	`[{"type": "protein", "chain": "A", "sequence": "ACDEFGHIK"}]`	Molecules JSON list of {"type": "protein"\|"dna"\|"rna", "chain": "A", "sequence": "..."}.
`ligands_list` list	string textarea	no	`—`	Ligands (optional) One ligand SMILES per line.
`ligands_molecules` molecules	string textarea	no	`—`	Ligands (optional) One ligand SMILES per line.
`bonds`	string textarea	no	`—`	Covalent bonds (optional) JSON list of covalent bonds between the chains above, e.g. [{"atom1Chain":"A","atom1Idx":"32","atom1Atom":"C","atom2Chain":"B","atom2Idx":"1","atom2Atom":"N"}]. Chains are lettered A, B, C... in the order entered: protein chains first, then DNA, then RNA, then ligands.
`seeds`	string text	no	`101`	Model seeds Comma-separated seeds, e.g. "101,102"; each produces an independent set of samples.
`samples`	number number	no	`1`	Samples per seed minimum 1, maximum 16.
`steps`	number number	no	`200`	Diffusion steps minimum 1, maximum 1000.
`cycles`	number number	no	`10`	Recycling cycles minimum 1, maximum 30.
`use_guidance`	boolean checkbox	no	`false`	Use physics-aware guidance Training-free guidance for improved ligand plausibility; increases compute time.

Molecule entry keys

Key	Meaning
`type`	Which of the field's molecule types this entry is.
`sequence`	The residues, for a protein, dna, or rna entry.
`ligand`	A SMILES string or a CCD_ code, for a ligand entry.
`ion`	An ion code, for an ion entry.
`cyclic`	Whether a polymer chain is cyclic. Tools that cannot model one reject it rather than ignoring it.
`modifications`	Substitutions, as {"position": <1-indexed integer>, "residue": "<CCD code>"} objects.

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/opendde/ \
  -H 'Content-Type: application/json' \
  -d '{
  "task": "sequence",
  "job_name": "opendde-demo",
  "sequence_molecules": "[{\"type\": \"protein\", \"sequence\": \"ACDEFGHIK\", \"cyclic\": false, \"modifications\": []}]",
  "bonds": "",
  "seeds": "101",
  "samples": 1,
  "steps": 200,
  "cycles": 10,
  "use_guidance": false
}'

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.