Property prediction · Protein Design

ThermoMPNN API

Predict the stability change of point mutations in a protein structure.

Runs ThermoMPNN, a ProteinMPNN-derived graph network trained by transfer learning to predict ddG for point mutants. custom_inference.py always scores every substitution at every position of a chain (a saturation scan); a named list of mutations is served by filtering that scan down to the requested substitutions rather than by asking the tool for them specifically, which its own CLI has no option for.

Web form Documentation ↗ Source code ↗

Submit POST /api/thermompnn/

Queues a run and returns 202 with the job.

Schema GET /api/thermompnn/

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
`scan` default	Saturation scan
`mutations`	Named mutations

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	`thermompnn-demo`	Job name
`pdb`	string file	yes	`HEADER PASTE A PROTEIN PDB HERE`	Protein PDB file types .pdb,.ent.
`chain`	string text	yes	`A`	Chain The chain the mutations are scored in; the rest of the structure is context. up to 4 characters.
`mutations` mutations	string textarea	yes	`T27A H31Q Y100F`	Mutations One per line, as wild-type residue, position, and mutant residue, for example T27A. Prefix with a chain and a colon to override the chain above.
`top_k` scan	number number	no	`20`	Top mutations to highlight Return the K most stabilising substitutions alongside the full table. 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/thermompnn/ \
  -H 'Content-Type: application/json' \
  -d '{
  "task": "scan",
  "job_name": "thermompnn-demo",
  "pdb": "HEADER    PASTE A PROTEIN PDB HERE",
  "chain": "A",
  "top_k": 20
}'

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.