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boltzgen

boltzgen is a skill for Claude Code, Codex from zongtingwei/Bioclaw_Skills_Hub. It costs 108 tokens per session (2,405 once invoked), scanned A, original, MIT.

A protein-design tool that uses a diffusion model to create complete protein structures, including side chains and nearby small molecules.

In plain words
What is it for?
Designing proteins that bind other proteins, peptides, small molecules, antibodies, or nanobodies from YAML configuration files.
Why use it?
It helps when backbone-only designs are not detailed enough, especially for precise binding shapes or ligand interactions.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one. Also seen: positional $N argument.

Needs its repository: it reads a path above its own folder, which exists only inside the repository. The line is **First time?** See [Installation Guide](../../docs/installation.md) to set up Modal and biomodals..

not rated 26repo 5mo ago A scan 108 tokens original MIT

Good fit Designing proteins that bind other proteins, peptides, small molecules, antibodies, or nanobodies from YAML configuration files.

Compare 6 skills from other repositories ↓
View source ↗ zongtingwei/Bioclaw_Skills_Hub
Install

Getting it into your agent

It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.

Clone the repo
git clone --depth 1 https://github.com/zongtingwei/Bioclaw_Skills_Hub
agentmods
npx agentmods add skills/zongtingwei/bioclaw_skills_hub/boltzgen

Made for: Claude Code, Codex.

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 boltzgen

README.md
[![agentmods](https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/boltzgen/github.svg)](https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/boltzgen)
Your own site
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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.

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Your own site · 80×15
<a href="https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/boltzgen"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/boltzgen.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 108 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,405 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 $0.00108 $0.02405
Opus 5 $0.00054 $0.01203
Sonnet 5 $0.00022 $0.00481
Haiku 4.5 $0.00011 $0.00241

Measured 12d ago against content hash 31163b83cf2c, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

boltzgen 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 12d 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.

skills/protein-design/skills/boltzgen/SKILL.md · 310 lines

How it starts

The opening of the file, as written. The whole thing — 310 lines — stays where its author put it; the contents beside it link to each section on GitHub.

BoltzGen All-Atom Design

Prerequisites

Requirement Minimum Recommended
Python 3.10+ 3.11
CUDA 12.0+ 12.1+
GPU VRAM 24GB 48GB (L40S)
RAM 32GB 64GB

How to run

First time? See Installation Guide to set up Modal and biomodals.

Option 1: Modal (recommended)

# Clone biomodals
git clone https://github.com/hgbrian/biomodals && cd biomodals

# Run BoltzGen (requires YAML config file)
modal run modal_boltzgen.py \
  --input-yaml binder_config.yaml \
  --protocol protein-anything \
  --num-designs 50

# With custom GPU
GPU=L40S modal run modal_boltzgen.py \
  --input-yaml binder_config.yaml \
  --protocol protein-anything \
  --num-designs 100

GPU: L40S (48GB) recommended | Timeout: 120min default

Available protocols: protein-anything, peptide-anything, protein-small_molecule, nanobody-anything, antibody-anything

Option 2: Local installation

git clone https://github.com/HannesStark/boltzgen.git
cd boltzgen
pip install -e .

python sample.py config=config.yaml

Option 3: Python API

from boltzgen import BoltzGen

model = BoltzGen.load_pretrained()
designs = model.sample(
    target_pdb="target.pdb",
    num_samples=50,
    binder_length=80
)

GPU: L40S (48GB) | Time: ~30-60s per design

Key parameters (CLI)

Parameter Default Description
--input-yaml required Path to YAML design specification
--protocol protein-anything Design protocol
--num-designs 10 Number of designs to generate
--steps all Pipeline steps to run (e.g., design inverse_folding)

YAML configuration

BoltzGen uses an entity-based YAML format where you specify designed proteins and target structures as entities.

Important notes:

  • Residue indices use label_seq_id (1-indexed), not author residue numbers
  • File paths are relative to the YAML file location
  • Target files should be in CIF format (PDB also works but CIF preferred)
  • Run boltzgen check config.yaml to verify your specification before running

Read the full file on GitHub · 310 lines

Files

What ships with it

2 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. 12d ago First seen · 310 lines · 108 tokens per session scan A 31163b83cf2c

Subscribe to this mod's changes

boltzgen is a skill published in the GitHub repository zongtingwei/Bioclaw_Skills_Hub (26 stars, last pushed 5mo ago), licensed MIT. It adds 108 tokens to every session and 2,405 once invoked, about $0.0005 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.

Scientificagentall-atombinderbioinformaticsdesign-toolsdiffusionopenclawsequence-designskillsstructure-design
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