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qfoldit-bionemo-agent-toolkit

qfoldit-bionemo-agent-toolkit is a skill for Claude Code from qfoldit/Protein-Design-MCP. It costs 159 tokens per session (1,675 once invoked), scanned A, original, Apache-2.0.

A toolkit for using five NVIDIA BioNeMo models, which are AI services for studying proteins, DNA, and small molecules. It covers protein-structure prediction, molecule docking, molecule generation, DNA-sequence generation, and structure or binding-affinity prediction.

In plain words
What is it for?
Use it to predict protein or molecular structures, test how a molecule may fit a protein, generate small molecules, create DNA sequences, and estimate structure or binding affinity.
Why use it?
It groups several molecular-modeling tasks behind documented calls and identifies the local containers, API keys, and GPU requirements needed to run them.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the qfoldit-skills plugin — 20 skills shipped together

not rated 1repo 2mo ago A scan 159 tokens original Apache-2.0

Good fit Use it to predict protein or molecular structures, test how a molecule may fit a protein, generate small molecules, create DNA sequences, and estimate structure or binding affinity.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/qfoldit/protein-design-mcp/bionemo-agent-toolkit
View source ↗ qfoldit/Protein-Design-MCP
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.

Any agent
npx skills add qfoldit/Protein-Design-MCP --skill bionemo-agent-toolkit
Clone the repo
git clone --depth 1 https://github.com/qfoldit/Protein-Design-MCP

Made for: Claude Code.

Or install qfoldit-skills, the plugin that ships this one along with the rest of its 20 skills.

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.

agentmods badge for qfoldit-bionemo-agent-toolkit

README.md
[![agentmods](https://agentmods.dev/badge/skills/qfoldit/protein-design-mcp/bionemo-agent-toolkit/github.svg)](https://agentmods.dev/skills/qfoldit/protein-design-mcp/bionemo-agent-toolkit)
Your own site
<a href="https://agentmods.dev/skills/qfoldit/protein-design-mcp/bionemo-agent-toolkit"><img src="https://agentmods.dev/badge/skills/qfoldit/protein-design-mcp/bionemo-agent-toolkit/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.

agentmods 80×15 button for qfoldit-bionemo-agent-toolkit

Your own site · 80×15
<a href="https://agentmods.dev/skills/qfoldit/protein-design-mcp/bionemo-agent-toolkit"><img src="https://agentmods.dev/badge/skills/qfoldit/protein-design-mcp/bionemo-agent-toolkit.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 159 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,675 The whole file, excluding the scripts and references it only reads on demand.
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.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00159 $0.01675
Opus 5.5 $0.00064 $0.00670
Sonnet 5.5 $0.00032 $0.00335
Haiku 4.5 $0.00016 $0.00168

Measured 2mo ago against content hash 1f13ab5e9ccd, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

qfoldit-bionemo-agent-toolkit 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 2mo ago.

The scan reads SKILL.md. This mod also ships 2 executable files (scripts/bionemo_client.py, scripts/smoke_test.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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/skills/bionemo-agent-toolkit/SKILL.md · 127 lines

How it starts

The opening of the file, as written. The whole thing — 127 lines — stays where its author put it; the contents beside it link to each section on GitHub.

qFoldIT BioNeMo Agent Toolkit

A client for five NVIDIA BioNeMo NIM microservices that do not already have their own MCP server, plus documented guidance on the one that does (AlphaFold3, via alphafold3_mcp).

Read references/api_reference.md before answering — exact endpoint paths and request/response shapes, each individually verified against NVIDIA's own documentation. Read references/alphafold3_mcp.md before saying anything about AlphaFold3 specifically — the integration approach there was corrected this session (see below).

What is implemented

Component Function Requirement
AlphaFold2 predict_protein_structure_af2(sequence, ...) Self-hosted NIM container, NGC API key
DiffDock dock_ligand(protein_pdb, ligand, ...) Self-hosted NIM container, NGC API key
MolMIM generate_molecules(seed_smiles, ...), get_molecule_embedding(smiles) Self-hosted NIM container, NGC API key
Evo 2 generate_dna_sequence_evo2(sequence, ...) Self-hosted NIM container, H100/H200-class GPU
Boltz-2 predict_structure_boltz2(polymers, ligands=..., ...) Self-hosted NIM container, >=48GB VRAM GPU

All five are implemented in scripts/bionemo_client.py as thin, honest requests-based HTTP clients against a self-hosted NIM container (default base_url="http://localhost:8000"). Every endpoint/payload shape was checked against NVIDIA's own docs during this session — see references/api_reference.md for citations per model. On any HTTP failure, the real error (status + body) is raised; no result is ever fabricated.

AlphaFold3 — different pattern, not reimplemented here

AlphaFold3 is not wrapped by this skill's own code. It already has a separate, real MCP server — MacromNex/alphafold3_mcp — which should be installed and connected in the same Claude session, the same way qFoldIT treats unity-mcp, UnrealClaude, or kit-usd-agents elsewhere: when an existing bridge already covers a tool, use it directly instead of duplicating it. See references/alphafold3_mcp.md for what was (and was not) verified about it this session — in particular, its exact exposed tool names were not confirmed; introspect the connected server's tool list rather than assuming names.

Read the full file on GitHub · 127 lines

Files

What ships with it

7 files beside SKILL.md 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.

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.

  1. 2mo ago First seen · 127 lines · 159 tokens per session scan A 1f13ab5e9ccd

Subscribe to this mod's changes

qfoldit-bionemo-agent-toolkit is a skill published in the GitHub repository qfoldit/Protein-Design-MCP (1 stars, last pushed 2mo ago), licensed Apache-2.0. It adds 159 tokens to every session and 1,675 once invoked, about $0.0006 per session on Opus 5.5. 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.

Data and AIScientific
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