Protein-design-skills setup

install

source · Clone the upstream repo

git clone https://github.com/adaptyvbio/protein-design-skills

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/adaptyvbio/protein-design-skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/setup" ~/.claude/skills/adaptyvbio-protein-design-skills-setup && rm -rf "$T"

manifest: skills/setup/SKILL.md

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

Once setup is complete, users can:

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
modal run modal_rfdiffusion.py --pdb target.pdb --contigs "A1-150/0 70-100" --num-designs 100

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

GPU selection

Set GPU with environment variable:

GPU=A10G modal run modal_rfdiffusion.py --pdb target.pdb --contigs "A1-100/0 50-80" --num-designs 10
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

GPU	VRAM	Best For
T4	16GB	ProteinMPNN, ESM
A10G	24GB	RFdiffusion, Chai
L40S	48GB	BoltzGen, BindCraft
A100	40-80GB	Large 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 Installation Guide