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setup
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By adaptyvbio/protein-design-skills (GitHub) · design · 173 stars · scanned at commit 59dd633
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.
Works with any agent that supports SKILL.md skills.
What this skill can do
Downloads and installs other software
The author does not mention this.
Found in 18 places.
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- skills/setup/SKILL.md, line 75
pip install uv - skills/setup/SKILL.md, line 83
pip install modal - docs/getting-started.md, line 34
pip install modal - docs/getting-started.md, line 64
uvx modal run modal_boltzgen.py --help - docs/getting-started.md, line 85
uvx modal run modal_boltzgen.py --input-yaml binder.yaml --protocol protein-anything --num-designs 5 - docs/getting-started.md, line 93
uvx modal run modal_boltzgen.py --input-yaml binder.yaml --protocol protein-anything --num-designs 50 - docs/getting-started.md, line 99
uvx modal run modal_bindcraft.py --input-pdb target.pdb --lengths "70,100" --number-of-final-designs 50 - docs/getting-started.md, line 105
uvx modal run modal_ligandmpnn.py --input-pdb backbone.pdb --params-str "--number_of_batches 8 --temperature 0.1" - docs/getting-started.md, line 111
uvx modal run modal_chai1.py --input-faa designs.fasta --out-dir predictions/ - docs/getting-started.md, line 114
uvx modal run modal_boltz.py --input-faa designs.fasta --out-dir predictions/ - docs/getting-started.md, line 121
GPU=L40S uvx modal run modal_boltzgen.py ... - docs/getting-started.md, line 122
GPU=A100 uvx modal run modal_chai1.py ... - docs/getting-started.md, line 123
MODAL_GPU=A100 uvx modal run modal_esmfold2.py ... - docs/getting-started.md, line 145
pip install modal - docs/getting-started.md, line 151
- Use a larger GPU: `GPU=A100 uvx modal run ...`
Runs commands on your computer
This is disclosed by the author in the skill's SKILL.md or README.
Found in 11 places.
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Sends data to these websites: files.rcsb.org
The author does not mention this.
Found in 1 place.
Safer alternatives
Low-risk skills in the same category (design) that look related. Check that one does what you need.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'setup' ] || [ -L ~/.agents/skills/'setup' ]; then echo 'A skill folder named setup already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/adaptyvbio/protein-design-skills' "$d" && git -C "$d" checkout --quiet '59dd63374314baa2fb1f9864f190775bd7466647' -- 'skills/setup' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/setup' ~/.agents/skills/'setup' && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'setup' ~/.claude/skills/'setup' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for adaptyvbio/protein-design-skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/adaptyvbio/protein-design-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 59dd633 | 77 |