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.
npx skills add adaptyvbio/protein-design-skills --skill setupgit clone --depth 1 https://github.com/adaptyvbio/protein-design-skillsWrote 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.
[](https://agentmods.dev/skills/adaptyvbio/protein-design-skills/setup)<a href="https://agentmods.dev/skills/adaptyvbio/protein-design-skills/setup"><img src="https://agentmods.dev/badge/skills/adaptyvbio/protein-design-skills/setup.svg" alt="Measured on agentmods" height="20"></a>- NVIDIA SkillSpector pass
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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00084 | $0.00995 |
| Opus 5 | $0.00042 | $0.00498 |
| Sonnet 5 | $0.00017 | $0.00199 |
| Haiku 4.5 | $0.00008 | $0.00100 |
Grade A, and why
setup 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.
How it starts
The opening of the file, as written. The whole thing — 159 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Setup Guide
Help users get their environment ready to run protein design tools.
Quick checklist
Run through this checklist when a user encounters setup issues:
| Step | Check | Fix |
|---|---|---|
| 1. Modal CLI | modal --version |
pip install modal |
| 2. Modal auth | modal token show |
modal setup |
| 3. biomodals | ls biomodals/modal_*.py |
git clone https://github.com/hgbrian/biomodals |
| 4. Test | cd biomodals && modal run modal_boltzgen.py --help |
See troubleshooting |
Diagnosing issues
Error: "modal: command not found"
Cause: Modal CLI not installed.
Fix:
pip install modal
Then restart the terminal or run hash -r.
Error: "Permission denied" or "Unauthorized"
Cause: Modal not authenticated.
Fix:
modal setup
This opens a browser. Click "Authorize" to complete authentication.
Error: "No such file or directory: modal_boltzgen.py"
Cause: biomodals repository not cloned or not in correct directory.
Fix:
git clone https://github.com/hgbrian/biomodals
cd biomodals
Error: "uvx: command not found"
Cause: uvx is an optional wrapper from the uv package. It's not required.
Fix: Run modal directly (recommended):
modal run modal_boltzgen.py --help
Or install uv if you prefer using uvx:
pip install uv
Full setup steps
Step 1: Install Modal CLI
pip install modal
Verify: modal --version
Step 2: Authenticate Modal
modal setup
This opens a browser. Click "Authorize".
Verify: modal token show
Step 3: Clone biomodals
git clone https://github.com/hgbrian/biomodals
cd biomodals
Verify: ls modal_*.py should show files like modal_boltzgen.py
Step 4: Test the Setup
cd biomodals
modal run modal_boltzgen.py --help
Expected: Usage instructions appear showing --input-yaml, --protocol, --num-designs options.
Common workflows after setup
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 · 159 lines · 84 tokens per session scan A 93b77bc9d3bb
setup is a skill published in the GitHub repository adaptyvbio/protein-design-skills (158 stars, last pushed 2mo ago), licensed MIT. It adds 84 tokens to every session and 995 once invoked, about $0.0004 per session on Opus 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 2026-08-30.
Other skills, from other repositories
setup
First-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with "file not found" or "modal: command not found", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or…
setup
First-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with "file not found" or "modal: command not found", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or…
setup
First-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with "file not found" or "modal: command not found", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or…
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protein-binder-design
Design and validate de novo protein binders with the current NVIDIA BioNeMo Agent Toolkit workflow, while adapting honestly when NVIDIA-hosted credentials are unavailable.
provider-setup
Reports which delegation CLIs are installed and authenticated, installs missing ones, and stores the result. Use before delegating or when a provider errors.