Diffdock Nim
Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses...
Install
npx skills add NVIDIA/skills --skill diffdock-nim -g -a claude-code -y- Repository
- NVIDIA/skills3.8k
- Category
- DevOps
- Updated
- 5d ago
- License
- Apache-2.0 AND CC-BY-4.0
- Context cost
- Lightabout 959 tokens
- Runs scripts
- No, instructions only
What it does
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.
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
Protein receptor must be ATOM records only. Strip headers, water, and HETATM.
