What is protein-structure-design-boltzgen?

A protein-design workflow that uses an all-atom diffusion model to create protein structures, including side chains and designs around small molecules. It is configured with YAML files, which are structured text settings files.

Use it to design protein binders, specify target molecules and binding sites, check design configurations, and generate sets of candidate structures on a suitable GPU.

It supports designs where the exact arrangement of atoms and binding geometry matters, rather than designing only the protein backbone.

protein-structure-design-boltzgen — Skill for Claude Code and Codex by

About the project

OpenBioMed is an agent platform and toolkit collection for biomedical research and drug discovery, covering areas such as molecular design, protein analysis, and single-cell data analysis. It is intended for researchers and provides the biomedical skills listed in the catalogue as workflows for Claude Code.

PharMolix/OpenBioMed · 1,105 stars · on GitHub

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/PharMolix/OpenBioMed

agentmods

npx agentmods add skills/pharmolix/openbiomed/protein-structure-design-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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/pharmolix/openbiomed/protein-structure-design-boltzgen/github.svg)](https://agentmods.dev/skills/pharmolix/openbiomed/protein-structure-design-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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/pharmolix/openbiomed/protein-structure-design-boltzgen"><img src="https://agentmods.dev/badge/skills/pharmolix/openbiomed/protein-structure-design-boltzgen.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 89 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 2,685 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. Third-party audits

NVIDIA SkillSpector pass 7 Sept 2026

How audits are shown

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.

Model	Per session	Once invoked
Fable 5.1	$0.00089	$0.02685
Opus 5	$0.00044	$0.01342
Sonnet 5	$0.00018	$0.00537
Haiku 4.5	$0.00009	$0.00268

Measured 13d ago against content hash cfd43de787d7, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

protein-structure-design-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 13d 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-structure-design-boltzgen/SKILL.md · 409 lines

How it starts

The opening of the file, as written. The whole thing — 409 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+	3.12
CUDA	12.0+	12.2
GPU VRAM	24GB	80GB (A800)
RAM	32GB	64GB

How to run

Local installation

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

Binder design according to the input YAML file

boltzgen run example/vanilla_protein/1g13prot.yaml \
  --output workbench/test_run \
  --protocol protein-anything \
  --num_designs 10 \
  --budget 2
# --num_designs is the number of intermediate designs. In practice you will want between 10,000 - 60,000
# --budget is how many designs should be in the final diversity optimized set

YAML configuration

BoltzGen uses an entity-based YAML format to specify what to design and what the target is.

Important notes:

Residue indices use label_seq_id (1-indexed), not auth_seq_id
File paths are relative to the YAML file location
Run boltzgen check config.yaml to verify before running
View in Molstar to confirm binding site is correctly specified

Entity Types

Designed Protein

entities:
  - protein:
      id: B                    # Chain ID for designed protein
      sequence: 80..140        # Variable length (80-140 residues)

Sequence specification:

80..140 - random length between 80 and 140 residues
80 - exactly 80 designed residues
AAAVVV20PPP - specific residues with 20 designed in middle
3..5C6C3 - designed residues with specific cysteines

Target from File

entities:
  - file:
      path: target.cif        # CIF or PDB file (relative to YAML)
      include:                 # Which chains/residues to include
        - chain:
            id: A
            res_index: 2..50,55..  # Optional: specific residues
      binding_types:           # Where design should bind
        - chain:
            id: A
            binding: 45,67,89  # Binding site residues
      structure_groups: "all"  # Optional: structure specification

Read the full file on GitHub · 409 lines

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.

13d ago First seen · 409 lines · 89 tokens per session scan A cfd43de787d7

Subscribe to this mod's changes

protein-structure-design-boltzgen is a skill published in the GitHub repository PharMolix/OpenBioMed (1,105 stars, last pushed 1mo ago), licensed MIT. It adds 89 tokens to every session and 2,685 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.

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protein-structure-design-boltzgen

Getting it into your agent

Wrote this? Show the measurements

What it costs to keep this loaded

Grade A, and why

Nothing flagged

How it starts

BoltzGen All-Atom Design

Prerequisites

How to run

Local installation

Binder design according to the input YAML file

YAML configuration

Entity Types

Designed Protein

Target from File

What this file has done since we first saw it

Other skills, from other repositories

boltzgen

boltzgen

boltzgen

boltzgen

rfdiffusion

bindcraft