Antibody design · Sequence prediction

AntiFold API

Structure-based antibody design using inverse folding

AntiFold predicts sequences which fit into an input antibody variable domain structure. The tool outputs residue log-likelihoods in CSV format, and can sample sequences to a FASTA format directly. Sampled sequences show high structural agreement with experimental structures. AntiFold is based on the ESM-IF1 model and is fine-tuned on solved and predicted antibody structures from SAbDab and OAS.

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Submit POST /api/antifold/

Queues a run and returns 202 with the job.

Schema GET /api/antifold/

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 AN IMGT-NUMBERED PDB HERE`	IMGT-numbered PDB file types .pdb,.ent.
`heavy_chain`	string text	yes	`H`	Heavy-chain ID up to 4 characters.
`light_chain`	string text	yes	`L`	Light-chain ID up to 4 characters.
`antigen_chain`	string text	no	`—`	Antigen-chain ID (optional)
`num_sequences`	number number	no	`10`	Sequences to sample minimum 1, maximum 1000.
`sampling_temperature`	number number	no	`0.2`	Sampling temperature minimum 0.01, maximum 2, step 0.05.

Example

A request that runs

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

curl -X POST https://athanortools.com/api/antifold/ \
  -H 'Content-Type: application/json' \
  -d '{
  "pdb": "HEADER    PASTE AN IMGT-NUMBERED PDB HERE",
  "heavy_chain": "H",
  "light_chain": "L",
  "antigen_chain": "",
  "num_sequences": 10,
  "sampling_temperature": 0.2
}'

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.
`cancelled`	Abandoned at the submitter's request; there is no result. A job cancelled before its turn never ran at all.

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 tool 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.