Genie 3 API

Generate all-atom protein-binder backbones against a target.

Builds a one-target Genie 3 binder-design problem and runs its target-conditioned generation stage.

Web form Home page ↗ Source code ↗

Submit POST /api/genie3/

Queues a run and returns 202 with the job.

Schema GET /api/genie3/

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	`genie3-demo`	Job name
`target_pdb`	string file	yes	`HEADER PASTE A TARGET PDB HERE`	Target PDB file types .pdb,.ent.
`target_sequence`	string textarea	yes	`MVTAYIAKQRQISFVKSHFSRQDILDLWIYHTQGYFP`	Target sequence
`target_selection`	string text	yes	`A1-40`	Target chain and residues Comma-separated PDB selections such as A1-40 or A2-158,B4-90.
`hotspots`	string text	yes	`A10,A20,A30`	Interface hotspots Comma-separated target chain/residue identifiers.
`minimum_length`	number number	no	`80`	Minimum binder length minimum 20, maximum 500.
`maximum_length`	number number	no	`120`	Maximum binder length minimum 20, maximum 500.
`num_samples`	number number	no	`1`	Binder candidates 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/genie3/ \
  -H 'Content-Type: application/json' \
  -d '{
  "job_name": "genie3-demo",
  "target_pdb": "HEADER    PASTE A TARGET PDB HERE",
  "target_sequence": "MVTAYIAKQRQISFVKSHFSRQDILDLWIYHTQGYFP",
  "target_selection": "A1-40",
  "hotspots": "A10,A20,A30",
  "minimum_length": 80,
  "maximum_length": 120,
  "num_samples": 1
}'

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.