diffdock-nim skill | PlugMCP

diffdock-nim

NVIDIA4.0kstars

Developer ToolsKnowledge Memory

1---2name: diffdock-nim3description: >4---56# skills/bionemo-diffdock-nim/SKILL.md

SKILL.mdAgent skill

Transport: File
Status: Listed

SKILL.md

Install

The skill file stays in the publisher's repository.

Paste the copied command in a terminal. It installs this SKILL.md into that agent.

shterminal

1npx skills add NVIDIA/skills --skill bionemo-diffdock-nim -a cursor -y

Paste the copied command in a terminal. It installs this SKILL.md into that agent.

shterminal

1npx skills add NVIDIA/skills --skill bionemo-diffdock-nim -a claude-code -y

Paste the copied command in a terminal. It installs this SKILL.md into that agent.

shterminal

1npx skills add NVIDIA/skills --skill bionemo-diffdock-nim -a codex -y

Paste the copied command in a terminal. It installs this SKILL.md into that agent.

shterminal

1npx skills add NVIDIA/skills --skill bionemo-diffdock-nim -a grok -y

Send the copied message in a Grok Bot chat. The Bot fetches this SKILL.md from GitHub and adds it to the skills all your Bots share.

txtGrok Bot chat

1Install this skill: https://github.com/NVIDIA/skills/tree/HEAD/skills/bionemo-diffdock-nim

Download skill skills/bionemo-diffdock-nim/SKILL.md on GitHub

skills/bionemo-diffdock-nim/SKILL.mdMarkdown · UTF-8

Skill facts

Agent skill

File: skills/bionemo-diffdock-nim/SKILL.md
Publisher: NVIDIA
Hosting

FAQ

Questions

From the publisher

SKILL.md

name: diffdock-nim
description: 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.
license: Apache-2.0 AND CC-BY-4.0
compatibility: requests>=2.28
allowed-tools: Bash, Read, Write, AskUserQuestion

DiffDock NIM

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

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

Prepare Inputs

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")

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()

diffdock-nim

Install

Skill facts

Questions

How do I install diffdock-nim?

Where does diffdock-nim live?

Which agents can use diffdock-nim?

SKILL.md

DiffDock NIM

Choose Mode

Local Docker

Prepare Inputs

Request Pattern

Save And Report Output

Limits And Troubleshooting