Structure prediction · Cheminformatics

PLACER API

Generate an ensemble of protein-ligand poses and side-chain conformations.

Runs PLACER (Protein-Ligand Atomistic Conformational Ensemble Resolver), a graph network that denoises corrupted atomic coordinates back to plausible ones. Given a structure and approximate knowledge of the binding site, it samples an ensemble of ligand poses and side-chain conformations rather than a single answer, with a predicted uncertainty (prmsd) per sample.

Web form Documentation ↗ Source code ↗

Submit POST /api/placer/

Queues a run and returns 202 with the job.

Schema GET /api/placer/

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	`placer-demo`	Job name
`structure_file`	string file	yes	`HEADER PASTE A PROTEIN-LIGAND STRUCTURE HERE`	Structure (PDB or mmCIF) Only mmCIF files from RCSB are correctly parsed; PDB is the safer choice otherwise. file types .pdb,.ent,.cif.
`num_samples`	number number	no	`10`	Samples 50-100 is a good number for docking; fewer is fine for side-chain conformations alone. minimum 1, maximum 500.
`predict_ligand`	string text	no	`—`	Ligands to predict (optional) Comma-separated ligand IDs, as name3, name3-resno, or chain-name3-resno. Empty predicts every ligand present.
`fixed_ligand`	string text	no	`—`	Ligands to hold fixed (optional) Comma-separated ligand IDs kept at their input coordinates instead of being predicted.
`target_res`	string text	no	`—`	Crop-center residue (optional) A protein residue, as chain-resno. Required when the input has no ligand at all. up to 40 characters.
`exclude_common_ligands`	boolean checkbox	no	`false`	Exclude common crystallography additives Drops solvents and crystallography additives (AlphaFold 3's exclusion list) before predicting.
`predict_multi`	boolean checkbox	no	`false`	Predict every allowed ligand Scores every eligible ligand rather than only the ones named in predict_ligand.
`rerank`	string select	no	`prmsd`	Rank output by One of: `prmsd`, `plddt`, `plddt_pde`, `none`.
`use_small_molecule`	boolean checkbox	no	`true`	Include the small molecule Off predicts side chains only (apo), ignoring any ligand in the input.

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/placer/ \
  -H 'Content-Type: application/json' \
  -d '{
  "job_name": "placer-demo",
  "structure_file": "HEADER    PASTE A PROTEIN-LIGAND STRUCTURE HERE",
  "num_samples": 10,
  "predict_ligand": "",
  "fixed_ligand": "",
  "target_res": "",
  "exclude_common_ligands": false,
  "predict_multi": false,
  "rerank": "prmsd",
  "use_small_molecule": true
}'

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.