Tools · Computational Biology

AutoDock Vina

High performance molecular docking and virtual screening for drug discovery

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Prices, workflows, and method papers Open 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.

AutoDock Vina `autodockvina`

Job type: autodockvina
Hardware: cpu (default)t4l4a10l40sa100-40gba100-80gbh100h200b200
Typical runtime: 15 min on CPU

Payload

Payload fields
Field	Type	Description
`pdb_id`	`string`	RCSB PDB id when not uploading protein. Limits: `min length 1`
`protein`	`file_object`	Uploaded protein structure.
`protein_download_format`	`string`	Default: `"pdb"`One of: `"pdb", "cif"`
`ligand`	`file_object`
`ligands[]`	`file_object[]`	Limits: `min items 1`
`pockets`	`integer \| string`	P2Rank pocket selection: positive integer or 'all'.
`boxes`	`file_object`	JSON table of docking boxes from pocket-detect (center + size per row).
`center[]`	`number[]`	Limits: `min items 3, max items 3`
`size[]`	`number[]`	Limits: `min items 3, max items 3`
`exhaustiveness`	`integer`	Default: `8`Limits: `≥ 1`
`num_modes`	`integer`	Default: `9`Limits: `≥ 1`
`energy_range`	`integer`	Default: `3`Limits: `≥ 0`
`box_padding`	`number`	Default: `10`Limits: `≥ 0`
`gpu_threads`	`integer`	Default: `8000`Limits: `≥ 1`
`skip_preprocessing`	`boolean`
`p2rank_path`	`string`

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>",
    },
    "ligand": {"name": "ligand.sdf", "content_b64": "<file contents, base64>"},
    "center": [0, 0, 0],
    "size": [20, 20, 20],
    "exhaustiveness": 1,
    "num_modes": 1,
}

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

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

curl -X POST "https://api.cognichem.com/api/v1/jobs/submit" \
  -H "X-Api-Key: $COGNICHEM_API_KEY" \
  -H "Idempotency-Key: $(uuidgen)" \
  -H "Content-Type: application/json" \
  -d '{
  "job_name": "my-autodockvina-run",
  "job_type": "autodockvina",
  "payload": {
    "protein": {
      "name": "protein.pdb",
      "content_b64": "<file contents, base64>"
    },
    "ligand": {
      "name": "ligand.sdf",
      "content_b64": "<file contents, base64>"
    },
    "center": [
      0,
      0,
      0
    ],
    "size": [
      20,
      20,
      20
    ],
    "exhaustiveness": 1,
    "num_modes": 1
  },
  "resource": "cpu"
}'

{
  "protein": {
    "name": "protein.pdb",
    "content_b64": "<file contents, base64>"
  },
  "ligand": {
    "name": "ligand.sdf",
    "content_b64": "<file contents, base64>"
  },
  "center": [
    0,
    0,
    0
  ],
  "size": [
    20,
    20,
    20
  ],
  "exhaustiveness": 1,
  "num_modes": 1
}

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

Workflow inputs

Table · optionalJSON
Molecules (list)SDF, MOL, MOL2, PDBQT
Protein structurePDB

Workflow outputs

ArchiveZIP
Docked posesPDBQT

Run it from the API

AutoDock Vina autodockvina

AutoDock Vina `autodockvina`