Structure prediction · Antibody design

ImmuneBuilder API

Predict an antibody, nanobody, or TCR structure in seconds.

Runs ABodyBuilder2, NanoBodyBuilder2, or TCRBuilder2 on the supplied variable-domain sequences. These are single-sequence models with no MSA or template search, so a structure comes back in seconds rather than the minutes a general folding model needs.

Web form Home page ↗ Source code ↗

Submit POST /api/immunebuilder/

Queues a run and returns 202 with the job.

Schema GET /api/immunebuilder/

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
`antibody` default	Antibody (Fv)
`nanobody`	Nanobody (VHH)
`tcr`	T-cell receptor

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	`immunebuilder-demo`	Job name
`heavy_sequence` antibody	string textarea	yes	`EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAED …`	Heavy-chain sequence Variable domain only; constant domains are not modelled.
`light_sequence` antibody	string textarea	yes	`DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQ …`	Light-chain sequence
`vhh_sequence` nanobody	string textarea	yes	`EVQLVESGGGLVQPGGSLRLSCAASGRTFSYNPMGWFRQAPGKGRELVAAISRTGGSTYYPDSVEGRFTISRDNAKRMVYLQMNSLRAED …`	VHH sequence
`alpha_sequence` tcr	string textarea	yes	`QSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQLLLKYYSGDPVVQGVNGFEAEFSKSNSSFHLRKASVHWSDSAVYFC …`	TCR alpha-chain sequence
`beta_sequence` tcr	string textarea	yes	`NAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYF …`	TCR beta-chain sequence
`numbering_scheme`	string select	no	`imgt`	Numbering scheme How the residues of the returned structure are numbered. One of: `imgt`, `chothia`, `kabat`, `aho`, `martin`, `wolfguy`, `raw`.
`n_threads`	number number	no	`0`	CPU threads for refinement 0 refines on the GPU; any other value forces OpenMM onto that many CPU threads. minimum 0, maximum 64.
`no_sidechain_bond_check`	boolean checkbox	no	`false`	Skip the strained-bond check Slightly faster, at the risk of an occasional unphysical side chain.
`original_weights` tcr	boolean checkbox	no	`false`	Use the original TCRBuilder2 weights Off by default, which uses the newer TCRBuilder2+ weights.

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/immunebuilder/ \
  -H 'Content-Type: application/json' \
  -d '{
  "task": "antibody",
  "job_name": "immunebuilder-demo",
  "heavy_sequence": "EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS",
  "light_sequence": "DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK",
  "numbering_scheme": "imgt",
  "n_threads": 0,
  "no_sidechain_bond_check": 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.