Antibody design · Protein Design · Binder design

Germinal API

Design de novo antibodies against a chosen epitope on a target structure.

Runs the Germinal pipeline, which hallucinates VHH or scFv binders through AlphaFold-Multimer under antibody language model guidance and then filters the trajectories on its structural and sequence criteria. Germinal's own configuration is a set of named Hydra profiles rather than a flat set of flags; this writes a target profile for the submitted structure and selects the matching run and filter profiles for the chosen binder format.

Web form Documentation ↗ Source code ↗

Submit POST /api/germinal/

Queues a run and returns 202 with the job.

Schema GET /api/germinal/

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
`job_name`	string text	no	`germinal-demo`	Job name
`target_pdb`	string file	yes	`HEADER PASTE A TARGET ANTIGEN PDB HERE`	Target antigen PDB file types .pdb,.ent,.cif.
`target_chain`	string text	yes	`A`	Target chain up to 4 characters.
`target_hotspots`	string text	yes	`A56,A57,A58`	Epitope hotspots Comma-separated target residues that define the epitope, for example A56,A57,A58.
`binder_format`	string select	no	`vhh`	Binder format One of: `vhh`, `scfv`.
`max_trajectories`	number number	no	`10`	Trajectories to run Hallucination trajectories attempted; most are discarded by the filters. minimum 1, maximum 10000.
`max_passing_designs`	number number	no	`2`	Designs to keep The run stops once this many designs have passed every filter. minimum 1, 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/germinal/ \
  -H 'Content-Type: application/json' \
  -d '{
  "job_name": "germinal-demo",
  "target_pdb": "HEADER    PASTE A TARGET ANTIGEN PDB HERE",
  "target_chain": "A",
  "target_hotspots": "A56,A57,A58",
  "binder_format": "vhh",
  "max_trajectories": 10,
  "max_passing_designs": 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.

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.