# Diffdock Nim

Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses...

- Repository: https://github.com/NVIDIA/skills (3812 stars)
- Category: DevOps
- License: Apache-2.0 AND CC-BY-4.0
- Last updated: 2026-10-30
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add NVIDIA/skills --skill diffdock-nim -g -a claude-code -y`
Codex: `npx skills add NVIDIA/skills --skill diffdock-nim -g -a codex -y`
Cursor: `npx skills add NVIDIA/skills --skill diffdock-nim -g -a cursor -y`
Gemini CLI: `npx skills add NVIDIA/skills --skill diffdock-nim -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add NVIDIA/skills`

## 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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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`](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.

The rest: https://github.com/NVIDIA/skills/blob/HEAD/skills/bionemo-diffdock-nim/SKILL.md