Openfold2 Nim

What it does

When your agent uses it

• NVIDIAs BioNeMo NIM microservice for monomer protein structure prediction
• Mentions OpenFold2
• AlphaFold2-like monomer folding
• Protein sequence-to-structure prediction

Example prompts

• “/openfold2-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

Openfold2 Nim loads about 1.8k tokens when it runs, and up to ~5k if it reads all its reference files. Until then it costs about 80 tokens; SKILL.md has 612 words of instructions outside code blocks.

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

~80

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

~1.8k

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

~5k

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:43

  `LOCAL_NIM_CACHE`. A repo-root `.env` file may be sourced as a local override.

• NoteMentions a .env fileSKILL.md:52

  For the exact startup preflight (`.env` sourcing, `NGC_API_KEY`/`NVIDIA_API_KEY`

• NoteMentions a .env fileSKILL.md:56

  not drop `.env`, `NGC_API_KEY`, `LOCAL_NIM_CACHE`, or the no-auth local request.

• 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). 612 words, ~1,802 tokens.

name

openfold2-nim

description

Use this skill for OpenFold2, NVIDIA's BioNeMo NIM microservice for monomer protein structure prediction. Invoke whenever the user mentions OpenFold2, AlphaFold2-like monomer folding, protein sequence-to-structure prediction, A3M MSAs, mmCIF templates, hosted NVIDIA API calls, 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

import os
import requests

hosted = True
url = (
    "https://health.api.nvidia.com/v1/biology/openfold/openfold2/predict-structure-from-msa-and-template"
    if hosted
    else "http://localhost:8000/biology/openfold/openfold2/predict-structure-from-msa-and-template"
)
headers = {"Content-Type": "application/json"}
if hosted:
    headers["Authorization"] = f"Bearer {os.getenv('NGC_API_KEY')}"

seq = "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPT"
payload = {
    "sequence": seq,
    "input_id": "kras_fragment",
    "selected_models": [1],
    "relax_prediction": False,
    "alignments": {
        "uniref90": {
            "a3m": {
                "alignment": f">query\n{seq}",
                "format": "a3m",
            }
        }
    },
}

response = requests.post(url, headers=headers, json=payload, timeout=300)
response.raise_for_status()
result = response.json()

from pathlib import Path
import json

Path("openfold2_response.json").write_text(json.dumps(result, indent=2))

def save_strings(obj, prefix="openfold2"):
    i = 0
    if isinstance(obj, dict):
        for key, value in obj.items():
            if isinstance(value, str) and ("ATOM" in value or value.lstrip().startswith("data_")):
                i += 1
                ext = "cif" if value.lstrip().startswith("data_") else "pdb"
                Path(f"{prefix}_{key}_{i}.{ext}").write_text(value)
            elif isinstance(value, (dict, list)):
                i += save_strings(value, f"{prefix}_{key}")
    elif isinstance(obj, list):
        for idx, value in enumerate(obj, start=1):
            if isinstance(value, (dict, list)):
                i += save_strings(value, f"{prefix}_{idx}")
    return i

saved = save_strings(result)
print(f"saved {saved} structure artifact(s)")

© 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 12 other files (references) in skills/bionemo-openfold2-nim of NVIDIA/skills.

• SKILL.md
• BENCHMARK.md
• config/skillspector-baseline.yml
• evals/config.yml
• evals/evals.json
• 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/openfold2-nimskills/bionemo-agent-toolkit/skills/openfold2-nim