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Agent skill

Setup

by adaptyvbio in adaptyvbio/protein-design-skills

First-time setup for protein design tools. An agent skill from adaptyvbio/protein-design-skills.

MITAuto-check passedResearch & Science

Install Setup

skills CLI
$ npx skills add adaptyvbio/protein-design-skills --skill setup -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install adaptyvbio/protein-design-skills setup --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/adaptyvbio/protein-design-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/setup .claude/skills/setup && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
setup
GitHub stars
163
Used in
2 other repos
Token cost
~896 tokens
SKILL.md length
263 words
Files
1
Skills in repo
24
Repo updated
First seen
Licence
MIT

At a glance

First-time setup for protein design tools. An agent skill from adaptyvbio/protein-design-skills.

  • Works in 4 steps: Install Modal CLI → Authenticate Modal → Clone biomodals → …
  • User is new and hasnt run any tools yet
  • SKILL.md covers Quick checklist, Diagnosing issues, Full setup steps and Common workflows after setup, plus 2 more sections
  • Calls modal, pip and git; reaches github.com

What it does

Setup is an agent skill from adaptyvbio/protein-design-skills. 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 tools aren't working.

Its SKILL.md is about 900 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Protein structure and design. The repository describes itself as: Claude Code skills for protein design. The licence is MIT.

When your agent uses it

  • User is new and hasnt run any tools yet
  • Commands fail with file not found
  • Modal: command not found
  • Modal authentication errors occur

Example prompts

  • “t run any tools yet, (2) Commands fail with”
  • “modal: command not found”
  • “/setup”

Requirements

  • Python 3

Workflow steps

4 steps, taken from the step headings in SKILL.md.

  1. Install Modal CLI
  2. Authenticate Modal
  3. Clone biomodals
  4. Test the Setup

What it can do on your machine

Read from SKILL.md and the folder at commit 59dd633. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • modal
    • pip
    • git
    • python

    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:

    • github.com

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Setup loads about 896 tokens when it runs. Until then it costs about 86 tokens; SKILL.md has 263 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~86
When it runs · the whole SKILL.md, loaded when a task matches
~896

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

Auto-check passed

The automated check found no risky patterns in SKILL.md.

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 adaptyvbio/protein-design-skills at commit 59dd633, republished under its MIT licence (© adaptyvbio). 263 words, ~896 tokens.

Download SKILL.mdSave it as .claude/skills/setup/SKILL.md (or your agent's skills folder).
name
setup
description
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 tools aren't working.
license
MIT
category
utilities
tags
setup, onboarding, installation

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:

StepCheckFix
1. Modal CLImodal --versionpip install modal
2. Modal authmodal token showmodal setup
3. biomodalsls biomodals/modal_*.pygit clone https://github.com/hgbrian/biomodals
4. Testcd biomodals && modal run modal_boltzgen.py --helpSee troubleshooting

Diagnosing issues

Error: "modal: command not found"

Cause: Modal CLI not installed.

Fix:

bash
pip install modal

Then restart the terminal or run hash -r.

Error: "Permission denied" or "Unauthorized"

Cause: Modal not authenticated.

Fix:

bash
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:

bash
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):

bash
modal run modal_boltzgen.py --help

Or install uv if you prefer using uvx:

bash
pip install uv

Full setup steps

Step 1: Install Modal CLI
bash
pip install modal

Verify: modal --version

Step 2: Authenticate Modal
bash
modal setup

This opens a browser. Click "Authorize".

Verify: modal token show

Step 3: Clone biomodals
bash
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
bash
cd biomodals
modal run modal_boltzgen.py --help

Expected: Usage instructions appear showing --input-yaml, --protocol, --num-designs options.

Common workflows after setup

Once setup is complete, users can:

bash
cd biomodals

# Design binders with BoltzGen (requires YAML config)
modal run modal_boltzgen.py --input-yaml binder.yaml --protocol protein-anything --num-designs 50

# Generate backbones with RFdiffusion (official repo, not biomodals)
python run_inference.py inference.input_pdb=target.pdb contigmap.contigs=[A1-150/0 70-100] inference.num_designs=100

# Validate with Chai
modal run modal_chai1.py --input-faa designs.fasta

GPU selection

Set GPU with environment variable:

bash
GPU=L40S modal run modal_boltzgen.py --input-yaml config.yaml --num-designs 50
GPU=A100 modal run modal_chai1.py --input-faa complex.fasta
GPUVRAMBest For
T416GBProteinMPNN, ESM
A10G24GBRFdiffusion, Chai
L40S48GBBoltzGen, BindCraft
A10040-80GBLarge complexes

Modal free tier

Modal offers $30/month in free credits - enough for:

  • ~500 BoltzGen designs
  • ~2000 RFdiffusion backbones
  • ~1000 Chai predictions

Full documentation: See Getting started

© adaptyvbio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/setup of adaptyvbio/protein-design-skills.

Open the folder on GitHubat commit 59dd633

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in adaptyvbio/protein-design-skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Setup next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Setup compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Setup this skilladaptyvbio/protein-design-skills1632 repos~896Automated safety check: PassMIT
Msa Structure Prediction PipelineNVIDIA/skills3.5k1 repos~1.6kAutomated safety check: NotesApache-2.0
Interpro Databasemajiayu000/claude-skill-registry6662 repos~2.7kAutomated safety check: PassCC0-1.0
Fda Databasejaechang-hits/SciAgent-Skills3701 repos~4.5kAutomated safety check: PassCC0-1.0
Pdb Structure APIwentorai/research-plugins2981 repos~1.9kAutomated safety check: PassMIT
Dailymed Databasejaechang-hits/SciAgent-Skills3701 repos~6kAutomated safety check: PassCC0-1.0

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  • Protein Design Workflow

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  • Protein Qc

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Categories

Questions about Setup

What does Setup do?

First-time setup for protein design tools. An agent skill from adaptyvbio/protein-design-skills. Setup is an agent skill from adaptyvbio/protein-design-skills. First-time setup for protein design tools.

When should I use Setup?

Setup fits situations like: user is new and hasnt run any tools yet; commands fail with file not found; modal: command not found; modal authentication errors occur.

How do I install Setup in Claude Code?

Run `npx skills add adaptyvbio/protein-design-skills --skill setup -a claude-code`. Or copy the skill folder (skills/setup in adaptyvbio/protein-design-skills) into .claude/skills/setup in your project. Claude Code loads it when a task matches its description.

How do I install Setup in Codex?

Run `npx skills add adaptyvbio/protein-design-skills --skill setup -a codex`. Or copy the skill folder (skills/setup in adaptyvbio/protein-design-skills) into .agents/skills/setup in your project. Codex loads it when a task matches its description.

Can I use Setup in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add adaptyvbio/protein-design-skills --skill setup -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/setup, .gemini/skills/setup, .github/skills/setup and .opencode/skills/setup in your project.

What does Setup need to run?

Going by SKILL.md and its folder, Setup needs the command-line tools its instructions call (modal, pip, git and python). Our summary lists: Python 3.

Does Setup access the network?

SKILL.md names 1 domain. In commands or code: github.com; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Setup safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Setup use?

Setup is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Setup use?

About 896 tokens (SKILL.md is roughly 3.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Setup?

Skills that share tags, products or a category with Setup: Msa Structure Prediction Pipeline (NVIDIA/skills, 3.5k stars), Interpro Database (majiayu000/claude-skill-registry, 666 stars), Fda Database (jaechang-hits/SciAgent-Skills, 370 stars) and Pdb Structure API (wentorai/research-plugins, 298 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Setup?

adaptyvbio (a GitHub organization) maintains it in adaptyvbio/protein-design-skills, which has 163 GitHub stars. The repository holds 24 skills in this directory. The repository was last updated on June 11, 2026.

Source: adaptyvbio/protein-design-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.