Download skills/bionemo-boltz2-nim/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does boltz2-nim live?
The publisher keeps it at https://github.com/NVIDIA/skills.
Which agents can use boltz2-nim?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.
>
name: boltz2-nim
description: >
Use Boltz2 NIM for biomolecular structure prediction and binding affinity. Invoke for Boltz2, protein structures, protein-ligand/DNA/RNA complexes, SMILES or CCD ligands, pIC50/IC50 affinity scoring, mmCIF output, hosted NVIDIA API calls, or local Docker deployment.
license: Apache-2.0 AND CC-BY-4.0
compatibility: "requests>=2.28"
allowed-tools: Bash, Read, Write, AskUserQuestion
Boltz2 NIM
Predict biomolecular structures and optional ligand affinity. Use this
guide for first-pass hosted/local usage; load supplemental files only when
needed:
Read credentials from the environment only when needed. Check presence with
bool(os.getenv("NGC_API_KEY")); keep key values and Authorization headers out of
terminal output, logs, saved artifacts, and the final response. Avoid environment
dumps when diagnosing authentication. If the hosted key is absent, report the
missing variable before submitting a request.
Hosted requests use Authorization: Bearer $NGC_API_KEY. Supported local Docker
startup uses NGC_API_KEY (or NVIDIA_API_KEY via the preflight) for
registry login, entitlement checks, and first-run model downloads; pass it
into the container with -e NGC_API_KEY. Local inference requests use no
auth header after readiness. Warm-cache key-free startup varies by
image/version and should not be assumed.
Local Docker
For local setup answers, copy the preflight below before docker login,
docker run, readiness, and the no-auth local request. Do not invent a cache
default or drop the .env load or NVIDIA_API_KEY fallback.
set -a
[ -f .env ] && . ./.env
set +a
if [ -z "${NGC_API_KEY:-}" ] && [ -n "${NVIDIA_API_KEY:-}" ]; then
export NGC_API_KEY="$NVIDIA_API_KEY"
fi
: "${NGC_API_KEY:?Set NGC_API_KEY or NVIDIA_API_KEY}"
: "${LOCAL_NIM_CACHE:?Set LOCAL_NIM_CACHE}"
echo "$NGC_API_KEY" | docker login nvcr.io --username '$oauthtoken' --password-stdin
mkdir -p "${LOCAL_NIM_CACHE}"
chmod 755 "${LOCAL_NIM_CACHE}"
docker run --rm --name boltz2 --gpus all \
--shm-size=16G \
-e NGC_API_KEY \
-v "${LOCAL_NIM_CACHE}:/opt/nim/.cache" \
-p 8000:8000 \
nvcr.io/nim/mit/boltz2:1.6.0
Readiness:
until curl -sf http://localhost:8000/v1/health/ready; do sleep 5; done
First startup downloads about 30 GB of model weights.
Examples
Prediction Request
import os
import requests
HOSTED = True
url = (
"https://health.api.nvidia.com/v1/biology/mit/boltz2/predict"
if HOSTED else "http://localhost:8000/biology/mit/boltz2/predict"
)
headers = {"Content-Type": "application/json"}
if HOSTED:
api_key = os.getenv("NGC_API_KEY")
if not api_key:
raise SystemExit("NGC_API_KEY is required for the hosted API")
headers["Authorization"] = f"Bearer {api_key}"
payload = {
"polymers": [{
"id": "A",
"molecule_type": "protein",
"sequence": "MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPT",
}],
"recycling_steps": 3,
"sampling_steps": 50,
"diffusion_samples": 1,
"step_scale": 1.638,
"output_format": "mmcif",
}
response = requests.post(url, headers=headers, json=payload, timeout=300)
response.raise_for_status()
result = response.json()
Payload essentials:
Protein polymer: {"molecule_type": "protein", "sequence": "..."}.
DNA/RNA polymer: add another polymer with molecule_type"dna" or "rna".
Ligand by SMILES: {"id": "L1", "smiles": "CC(=O)OC1=CC=CC=C1C(=O)O"}.
Ligand by CCD: {"id": "L1", "ccd": "ATP"}.
Affinity: set "predict_affinity": True on exactly one ligand; report
affinity_pic50, affinity_pred_value, and affinity_probability_binary.
Precomputed A3M MSA goes under the protein polymer. The A3M record uses
alignment, format, and rank; do not use a stale data field.
Save every .cif artifact and read the confidence/affinity fields using the
snippet in references/examples.md under Save
Structures And Affinity. Visualize in PyMOL, ChimeraX, or UCSF Chimera. For
confidence/affinity sanity checks, read references/validation.md.
Local URL/auth: local path has no hosted auth header; wait on /v1/health/ready.
Local startup: use --gpus all, --shm-size=16G, and the /opt/nim/.cache mount.
How do I install boltz2-nim?
Download skills/bionemo-boltz2-nim/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does boltz2-nim live?
The publisher keeps it at https://github.com/NVIDIA/skills.
Which agents can use boltz2-nim?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.