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Antibody design · Sequence prediction

AbMPNN API

Design antibody sequences from a backbone structure.

Prepares an antibody-specific ProteinMPNN run using separately supplied AbMPNN weights.

Web form Home page ↗ Source code ↗
Submit POST /api/abmpnn/

Queues a run and returns 202 with the job.

Schema GET /api/abmpnn/

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

Runtime

ProteinMPNN checkout and separate AbMPNN model weights required · Python app (uv) · Moderate (s)

License

Permissive. Two licences, because this is ProteinMPNN's network run against someone else's weights: the ProteinMPNN code is MIT, and the AbMPNN weights are published by Exscientia on Zenodo under CC BY 4.0. Both allow commercial use with attribution.

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 AN ANTIBODY PDB HERE Antibody PDB file types .pdb,.ent.
designed_chains string text yes H L Chains to design Space-separated chain IDs; heavy chain first.
num_sequences number number no 8 Number of sequences minimum 1, maximum 1000.
temperature number number no 0.2 Sampling temperature minimum 0.01, maximum 1, step 0.05.
omit_amino_acids string text no X Amino acids to omit One-letter amino-acid codes.
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/abmpnn/ \
  -H 'Content-Type: application/json' \
  -d '{
  "pdb": "HEADER    PASTE AN ANTIBODY PDB HERE",
  "designed_chains": "H L",
  "num_sequences": 8,
  "temperature": 0.2,
  "omit_amino_acids": "X"
}'

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

statusMeaning
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

codeMeaning
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.