ProteinMPNN-ddG API

Predict the stability effects of every point mutation in a protein chain.

Runs ProteinMPNN-ddG with full sequence context and writes its saturation-mutagenesis scores as CSV.

Web form Home page ↗ Source code ↗

Submit POST /api/proteinmpnn_ddg/

Queues a run and returns 202 with the job.

Schema GET /api/proteinmpnn_ddg/

Returns this tool's metadata and the fields below, as 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
`pdb`	string file	yes	`HEADER PASTE A PROTEIN PDB HERE`	Protein PDB file types .pdb,.ent.
`chains`	string text	yes	`A`	Context chains Comma-separated chains; the first is predicted by default.
`chain_to_predict`	string text	no	`—`	Chain to predict Optional; defaults to the first context chain.
`model_name`	string select	no	`v_48_020`	Model One of: `v_48_002`, `v_48_010`, `v_48_020`, `v_48_030`.
`seed`	number number	no	`42`	Random seed minimum 0, maximum 2147483647.
`repeats`	number number	no	`1`	Model repeats minimum 1, maximum 100.
`without_ddg_correction`	boolean checkbox	no	`false`	Disable the published ddG correction Required when selecting a model other than v_48_020.
`top_k`	number number	no	`0`	Top mutations to highlight (optional) Return only the K most stability-improving mutations, ranked by predicted ddG. 0 returns the full table only. minimum 0, maximum 1000.

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/proteinmpnn_ddg/ \
  -H 'Content-Type: application/json' \
  -d '{
  "pdb": "HEADER    PASTE A PROTEIN PDB HERE",
  "chains": "A",
  "chain_to_predict": "",
  "model_name": "v_48_020",
  "seed": 42,
  "repeats": 1,
  "without_ddg_correction": false,
  "top_k": 0
}'

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.