What is qfoldit-skills?

A collection of 20 Claude skills for scientific simulation and digital-twin work, using a shared Universal Assembly Graph to describe scenes and systems.

Protein folding, quantum and chemical simulations, mining and corrosion studies, plant and material models, virtual reality, and scene export.

It provides task-specific guidance for connecting scientific models with engines and formats such as Unreal, Unity, OpenUSD, visionOS, and Three.js.

qfoldit-skills — Plugin for Claude Code by qfoldit

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Clone the repo

git clone --depth 1 https://github.com/qfoldit/Protein-Design-MCP

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/plugins/qfoldit/protein-design-mcp/claude-skills/github.svg)](https://agentmods.dev/plugins/qfoldit/protein-design-mcp/claude-skills)

Your own site

<a href="https://agentmods.dev/plugins/qfoldit/protein-design-mcp/claude-skills"><img src="https://agentmods.dev/badge/plugins/qfoldit/protein-design-mcp/claude-skills/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/plugins/qfoldit/protein-design-mcp/claude-skills"><img src="https://agentmods.dev/badge/plugins/qfoldit/protein-design-mcp/claude-skills.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session not measured What this adds to a session before it is invoked.

When invoked not measured The manifest loads nothing itself; its 20 skills cost 2,860 tokens a session between them.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Security

Grade A, and why

qfoldit-skills scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

claude-skills/.claude-plugin/plugin.json · 115 lines

How it starts

The opening of the file, as written. The whole thing — 115 lines — stays where its author put it; the contents beside it link to each section on GitHub.

{
  "name": "qfoldit-skills",
  "version": "1.2.0",
  "description": "Twenty Claude skills for qFoldIT: scientific simulation (VQE, protein folding, bio-mining, corrosion, MEOR, prospecting, plant growth, plastic pyrolysis, L-systems, NanoVer VR bridge, BioNeMo structure prediction) plus digital-twin/engine adapters (Unreal, Unity, Unigine, OpenUSD/Omniverse, Apple RealityKit/visionOS, Three.js/WebXR) and universal scene export, built on a shared Universal Assembly Graph (UAG) format.",
  "author": "qFoldIT",
  "license": "MIT",
  "repository": "https://github.com/qfoldit/skills",
  "homepage": "https://qfoldit.github.io/claude/",
  "keywords": [
    "science",
    "simulation",
    "chemistry",
    "biology",
    "quantum",
    "L-systems",
    "corrosion",
    "mining",
    "plastic pyrolysis",
    "digital twin",
    "unreal",
    "unity",
    "unigine",
    "omniverse",
    "usd",
    "visionos",
    "realitykit",
    "threejs",
    "webxr",
    "nanover",
    "vr"
  ],
  "skills": {
    "scene-export": {
      "description": "Converts an engine-agnostic scene description (molecules, L-system geometry) into universal files -- OBJ, glTF 2.0, standalone Three.js HTML, Godot 4.x GDScript -- for use outside the live MCP engine adapters",
      "path": "skills/scene-export"
    },
    "quantum": {
      "description": "Classical statevector VQE simulator (numpy), validated against a published H2/STO-3G benchmark (arXiv:2209.09564)",
      "path": "skills/quantum"
    },
    "qfold": {
      "description": "Hybrid quantum-classical 2D HP-lattice protein folding (Dill 1985) with QAOA-style circuit on Braket LocalSimulator",
      "path": "skills/qfold"
    },
    "bionemo-agent-toolkit": {
      "description": "AlphaFold2, DiffDock, MolMIM, Evo 2, Boltz-2 -- real HTTP clients against self-hosted NVIDIA BioNeMo NIM containers, verified against NVIDIA's own docs. AlphaFold3 is handled via the separate alphafold3_mcp MCP server, not reimplemented here. Compatible client,

Read the full file on GitHub · 115 lines

Contents

What it installs

The manifest is a name and a version. 20 skills travel with it, and installing the plugin installs all of them — 2,860 tokens a session between them. Each is measured on its own page, and each can be installed alone.

Files

What ships with it

1 file beside plugin.json in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

marketplace.json 320 B

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

8d ago First seen · 115 lines scan A 39d78631e494

Subscribe to this mod's changes

qfoldit-skills is a plugin published in the GitHub repository qfoldit/Protein-Design-MCP (1 stars, last pushed 12d ago), licensed Apache-2.0. Its token cost is not measured: this kind of file is read by the harness, not the model. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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