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    Tools · Computational Biology

    Binding-Site Detector

    Find ligandable pockets and emit Vina-shaped docking boxes for fold-to-dock workflows
    On this page

    Prices, workflows, and method papersOpen in the app

    Run it from the API

    Submit with Submit a job and the job_type below. Price it first with Estimate job reservation cost: submitting reserves that amount from your wallet, and the charge settles at the actual runtime.

    Binding-Site Detector pocket-detect

    Job type
    pocket-detect
    Hardware
    cpu (default)
    Typical runtime
    3 min on CPU

    Payload

    Payload fields
    FieldTypeDescription
    pdb_idstring

    RCSB PDB id when not uploading protein.

    Limits: min length 1

    proteinfile_object

    Uploaded protein structure (PDB or CIF).

    protein_download_formatstring

    Default: "pdb"One of: "pdb", "cif"

    methodstring

    Pocket engine. 'both' runs each engine and applies max_pockets per engine.

    Default: "p2rank"One of: "p2rank", "fpocket", "both"

    max_pocketsinteger | string

    Keep top-N pockets per engine (or all). If fewer are found, keep those. Error if zero.

    Default: 1

    box_paddingnumber

    Default: 10Limits: ≥ 0

    include_dummy_ligandboolean

    Default: true

    prefer_holo_ligandboolean

    Default: true

    reference_ligandfile_object

    Optional SDF override emitted as the chainable reference ligand.

    p2rank_pathstring
    fpocket_pathstring

    File fields take {"name": "x.pdb", "content_b64": "…"} or a stored artifact, {"$artifact": {"id": "art-…", "port": "…"}}. Files are up to 25 MiB each.

    Example

    from cognichem_client import CogniChem

client = CogniChem.from_env()  # reads COGNICHEM_API_KEY
payload = {
    "protein": {
        "name": "protein.pdb",
        "content_b64": "<file contents, base64>",
    },
    "method": "p2rank",
    "max_pockets": 1,
    "box_padding": 10,
}

estimate = client.jobs.estimate(job_type="pocket-detect", payload=payload, resource="cpu")
print(f"Reserves ${estimate.cost:.2f}")

job = client.jobs.submit(
    job_name="my-pocket-detect-run",
    job_type="pocket-detect",
    payload=payload,
    resource="cpu",
)
status = client.jobs.wait(job.process_id)
if status.status == "completed":
    client.jobs.result(job.process_id, save_path=".")

    Sample data from the job catalog; long values are shortened here. Each job_name must be unique among your jobs.

    Workflow inputs

    • Protein structurePDB, CIF
    • Molecules · optionalSDF

    Workflow outputs

    • ArchiveZIP
    • TableJSON
    • MoleculesSDF