Tools · Computational Biology

SurfDock

Surface-informed diffusion docking with a reference-ligand pocket and screen-model rescoring

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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.

SurfDock `surfdock`

Job type: surfdock
Hardware: t4l4a10 (default)l40sa100-40gba100-80gbh100h200b200
Typical runtime: 30 min on Nvidia A10

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.`name`	`string`	Limits: `min length 1`
protein.`filename`	`string`	Limits: `min length 1`
protein.`content_b64`	`string`	Limits: `min length 1`
protein.`content`	`any`
protein.`bytes`	`any`
`protein_format`	`string`	Default: `"pdb"`One of: `"pdb", "cif"`
`protein_download_format`	`string`	Default: `"pdb"`One of: `"pdb", "cif"`
`reference_ligand`	`file_object`	3D ligand bound in the target pocket (defines binding site).
reference_ligand.`name`	`string`	Limits: `min length 1`
reference_ligand.`filename`	`string`	Limits: `min length 1`
reference_ligand.`content_b64`	`string`	Limits: `min length 1`
reference_ligand.`content`	`any`
reference_ligand.`bytes`	`any`
`reference_ligand_format`	`string`	Default: `"sdf"`One of: `"sdf"`
`ligand`	`file_object`	Ligand structure file to dock (SDF).
ligand.`name`	`string`	Limits: `min length 1`
ligand.`filename`	`string`	Limits: `min length 1`
ligand.`content_b64`	`string`	Limits: `min length 1`
ligand.`content`	`any`
ligand.`bytes`	`any`
`ligand_smiles`	`string`	Ligand SMILES when not uploading a ligand file. Limits: `min length 1`
`ligand_format`	`string`	Default: `"sdf"`One of: `"sdf", "smiles"`
`num_poses`	`integer`	Number of docked poses to generate. Default: `20`Limits: `≥ 1, ≤ 100`
`num_rescored_poses`	`integer`	Number of top poses to energy-minimize and rescore with the SurfDock screen model. Default: `5`Limits: `≥ 1, ≤ 100`
`surfdock_options`	`object`	Optional passthrough bag for additional SurfDock CLI/flags.

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>",
    },
    "protein_format": "pdb",
    "reference_ligand": {
        "name": "reference_ligand.sdf",
        "content_b64": "<file contents, base64>",
    },
    "reference_ligand_format": "sdf",
    "ligand_smiles": "CCO",
    "ligand_format": "smiles",
    "num_poses": 1,
    "num_rescored_poses": 1,
}

estimate = client.jobs.estimate(job_type="surfdock", payload=payload, resource="a10")
print(f"Reserves ${estimate.cost:.2f}")

job = client.jobs.submit(
    job_name="my-surfdock-run",
    job_type="surfdock",
    payload=payload,
    resource="a10",
)
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-surfdock-run",
  "job_type": "surfdock",
  "payload": {
    "protein": {
      "name": "protein.pdb",
      "content_b64": "<file contents, base64>"
    },
    "protein_format": "pdb",
    "reference_ligand": {
      "name": "reference_ligand.sdf",
      "content_b64": "<file contents, base64>"
    },
    "reference_ligand_format": "sdf",
    "ligand_smiles": "CCO",
    "ligand_format": "smiles",
    "num_poses": 1,
    "num_rescored_poses": 1
  },
  "resource": "a10"
}'

{
  "protein": {
    "name": "protein.pdb",
    "content_b64": "<file contents, base64>"
  },
  "protein_format": "pdb",
  "reference_ligand": {
    "name": "reference_ligand.sdf",
    "content_b64": "<file contents, base64>"
  },
  "reference_ligand_format": "sdf",
  "ligand_smiles": "CCO",
  "ligand_format": "smiles",
  "num_poses": 1,
  "num_rescored_poses": 1
}

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

Workflow inputs

Molecules · optionalSDF
Protein structurePDB, CIF
MoleculesSDF

Workflow outputs

ArchiveZIP
Docked posesSDF

Run it from the API

SurfDock surfdock

SurfDock `surfdock`