diffdock-nim

Original：🇺🇸 English

Translated

Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets. Use for DiffDock, molecular docking, ligand docking, blind docking, SMILES or SDF ligands, ranked poses, confidence scores, hosted NVIDIA API, or local Docker deployment.

4installs

Sourcenvidia-bionemo/bionemo-agent-toolkit

Added on2026-08-21

NPX Install

npx skill4agent add nvidia-bionemo/bionemo-agent-toolkit diffdock-nim

SKILL.md Content

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DiffDock NIM

Predict protein-ligand binding poses with blind docking. Use this

SKILL.md

for first-pass hosted/local usage; load supplemental files only when needed:

```
references/api.md
```
: exact hosted/local endpoints, schemas, Docker flags.
```
references/science.md
```
: docking use cases, limits, and handoffs.
```
references/parameters.md
```
: ligand formats, pose counts, diffusion controls.
```
references/validation.md
```
: receptor, ligand, pose, and confidence checks.
```
references/examples.md
```
: compact hosted/local and pose-saving patterns.

Choose Mode

Ask only when context is unclear:

Hosted NVIDIA API or local Docker NIM?

Hosted:

https://health.api.nvidia.com/v1/biology/mit/diffdock

Local:

http://localhost:8000/molecular-docking/diffdock/generate

The hosted and local paths differ. Local has no

/v1/

prefix and uses the

/molecular-docking/

route. Hosted requests use

Authorization: Bearer $NGC_API_KEY

. Supported local Docker startup uses

NGC_API_KEY

(or

NVIDIA_API_KEY

via the preflight) for registry login, entitlement checks, and first-run model downloads; pass it into the container with

-e NGC_API_KEY

. Local inference requests use no auth header after readiness. Warm-cache key-free startup varies by image/version and should not be assumed.

Local Docker

For the exact local preflight (

.env

load,

NVIDIA_API_KEY

fallback,

LOCAL_NIM_CACHE

,

NVIDIA_VISIBLE_DEVICES=0

,

--shm-size=2G

, both

--ulimit

flags,

docker login

, and the

docker run

for

nvcr.io/nim/mit/diffdock:2.2.0

), copy the command block in

references/api.md

under Docker Reference verbatim.

Readiness:

bash

until curl -sf http://localhost:8000/v1/health/ready; do sleep 5; done

Prepare Inputs

Protein receptor must be ATOM records only. Strip headers, water, and HETATM.

python

from pathlib import Path
raw_pdb = Path("protein.pdb").read_text()
protein = "\n".join(line for line in raw_pdb.splitlines() if line.startswith("ATOM"))
if not protein:
    raise ValueError("protein.pdb has no ATOM records")

Ligand options:

SMILES:

ligand = "CC(=O)OC1=CC=CC=C1C(=O)O"

;

ligand_file_type = "txt"

.

SDF:

ligand = Path("ligand.sdf").read_text()

;

ligand_file_type = "sdf"

.

MOL2:
```
ligand_file_type = "mol2"
```
.

Do not use

"smiles"

as

ligand_file_type

; SMILES is

"txt"

.

Request Pattern

python

import os
import requests

HOSTED = True
url = (
    "https://health.api.nvidia.com/v1/biology/mit/diffdock"
    if HOSTED else "http://localhost:8000/molecular-docking/diffdock/generate"
)
headers = {"Content-Type": "application/json"}
if HOSTED:
    headers["Authorization"] = f"Bearer {os.getenv('NGC_API_KEY')}"

payload = {
    "protein": protein,
    "ligand": ligand,
    "ligand_file_type": ligand_file_type,
    "num_poses": 10,
    "time_divisions": 20,
    "steps": 18,
    "save_trajectory": False,
}
response = requests.post(url, headers=headers, json=payload, timeout=300)
response.raise_for_status()
result = response.json()

Save And Report Output

ligand_positions

and

position_confidence

are parallel ranked lists.

position_confidence[0]

is the rank-1 pose confidence.

Save the ranked pose SDFs using the snippet in

references/examples.md

under Save Ranked Poses.

View pose SDF files with the receptor in PyMOL, ChimeraX, or UCSF Chimera. For pose sanity checks and confidence caveats, read

references/validation.md

.

Limits And Troubleshooting

Max
```
num_poses
```
: 100. Max
```
time_divisions
```
: 20. Max
```
steps
```
: 18.
Single GPU; local minimum is about 24 GB VRAM.
```
422
```
: invalid
```
ligand_file_type
```
, invalid SMILES/SDF, or no ATOM records.
Empty poses: validate receptor ATOM records and ligand parseability.
Local URL 404 usually means the wrong hosted path or an accidental
```
/v1/
```
.