Diffdock Nim

What it does

When your agent uses it

• Molecular docking
• Confidence scores
• Hosted NVIDIA API
• Local Docker deployment

Example prompts

• “/diffdock-nim”

Requirements

• Python 3
• Docker
• A credential in NGC_API_KEY
• A credential in NVIDIA_API_KEY
• Compatibility (from SKILL.md): requests>=2.28
• Pre-approved tools (allowed-tools): Bash, Read, Write, AskUserQuestion

What it can do on your machine

Read from SKILL.md and the folder at commit 0e0d506. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves these tools, so the agent can use them without asking each time:

  • Bash
  • Read
  • Write
  • AskUserQuestion

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Shell commands in SKILL.md call:

  • docker

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Hosts in commands or code, which the agent is likely to contact:

  • health.api.nvidia.com

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names these keys or tokens, usually read from environment variables:

  • NGC_API_KEY
  • NVIDIA_API_KEY

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

• Compatibility

  requests>=2.28

  From compatibility in the SKILL.md frontmatter.

Context cost

Diffdock Nim loads about 1.1k tokens when it runs, and up to ~3.9k if it reads all its reference files. Until then it costs about 74 tokens; SKILL.md has 326 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~74

When it runs · the whole SKILL.md, loaded when a task matches

~1.1k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~3.9k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

• NoteMentions a .env fileSKILL.md:40

  For the exact local preflight (`.env` load, `NVIDIA_API_KEY` fallback,

• NotePre-approves every shell command (allowed-tools: Bash)SKILL.md

  allowed-tools: Bash, Read, Write, AskUserQuestion

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from NVIDIA/skills at commit 0e0d506, republished under its Apache-2.0 licence (© NVIDIA). 326 words, ~1,070 tokens.

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.

allowed-tools

Bash, Read, Write, AskUserQuestion

compatibility

requests>=2.28

license

Apache-2.0 AND CC-BY-4.0

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

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()

© NVIDIA, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 13 other files (references) in skills/bionemo-diffdock-nim of NVIDIA/skills.

• SKILL.md
• BENCHMARK.md
• config/skillspector-baseline.yml
• evals/config.yml
• evals/evals.json
• evals/files/protein.pdb
• evals/trigger_evals.json
• references/api.md
• references/examples.md
• references/parameters.md
• references/science.md
• references/validation.md
• skill-card.md
• skill.oms.sig

Open the folder on GitHubat commit 0e0d506

Used in 1 other repository

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in NVIDIA/skills, which our catalogue first saw on October 7, 2026.

• NVIDIA-BioNeMo/bionemo-agent-toolkitnim-skills/diffdock-nimskills/bionemo-agent-toolkit/skills/diffdock-nim