A model that predicts 3D structures of biomolecular complexes and estimates how strongly a molecule may bind. It works with proteins, DNA, RNA, ligands, and cyclic peptides, and can output common structure files such as PDB or mmCIF.

Use it to model protein–molecule complexes, estimate measures such as IC50 or binding free energy, screen compound libraries, add binding-pocket constraints, or study protein–DNA and protein–RNA interactions.

It combines structure prediction and binding-affinity estimation in one run, helping reduce the need for separate tools when screening or improving drug candidates.

boltz — Skill for Claude Code and Codex by naity/FM4Life

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/naity/FM4Life

agentmods

npx agentmods add skills/naity/fm4life/boltz

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/naity/fm4life/boltz/github.svg)](https://agentmods.dev/skills/naity/fm4life/boltz)

Your own site

<a href="https://agentmods.dev/skills/naity/fm4life/boltz"><img src="https://agentmods.dev/badge/skills/naity/fm4life/boltz/github.svg" alt="Measured on agentmods" height="20"></a>

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/naity/fm4life/boltz"><img src="https://agentmods.dev/badge/skills/naity/fm4life/boltz.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 133 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 2,467 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.

Model	Per session	Once invoked
Fable 5.1	$0.00133	$0.02467
Opus 5.5	$0.00053	$0.00987
Sonnet 5.5	$0.00027	$0.00493
Haiku 4.5	$0.00013	$0.00247

Measured 2mo ago against content hash d3b082f2a001, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

boltz 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 2mo ago.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/build_input.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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/boltz/SKILL.md · 282 lines

How it starts

The opening of the file, as written. The whole thing — 282 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Boltz-2: Biomolecular Structure and Binding Affinity Prediction

Overview

Boltz-2 is a biomolecular foundation model that jointly predicts complex 3D structure and binding affinity in a single inference pass. It is the first fully open-source model to approach AlphaFold 3-level structural accuracy while also providing quantitative affinity predictions 1000× faster than physics-based FEP methods.

Capability	Boltz-2	AlphaFold 3
Proteins, RNA, DNA, ligands	✓	✓
Binding affinity prediction	✓	✗
Pocket/contact constraints	✓	✗
Cyclic peptides	✓	✗
License	MIT (commercial OK)	CC-BY-NC-SA 4.0
Model weights	Freely available	Must apply to Google
Input format	YAML	JSON
Output format	mmCIF or PDB	mmCIF only

Installation

pip install boltz[cuda] -U

For CPU-only (slow, for testing):

pip install boltz -U

Requirements: Python ≥ 3.10, < 3.13; NVIDIA GPU recommended.

Quick Start

# Predict structure (auto-generate MSA via server)
boltz predict input.yaml --use_msa_server

# Predict structure + binding affinity
boltz predict complex.yaml --use_msa_server --diffusion_samples 5

# Multiple samples for ensemble
boltz predict input.yaml --use_msa_server --diffusion_samples 5

Input Format (YAML)

Boltz-2 uses YAML input files. See references/input-format.md for the full schema.

Single protein

version: 1
sequences:
  - protein:
      id: A
      sequence: MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGD

Protein–ligand complex

version: 1
sequences:
  - protein:
      id: A
      sequence: MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGD
      msa: ./msas/protein_a.a3m
  - ligand:
      id: B
      ccd: ATP
  - ligand:
      id: C
      ccd: MG

With binding affinity prediction

Add a properties block with one small molecule as the binder:

version: 1
sequences:
  - protein:
      id: A
      sequence: MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGD
      msa: ./msas/protein_a.a3m
  - ligand:
      id: B
      smiles: "CC(=O)Nc1ccc(O)cc1"
properties:
  - affinity:
      binder: B

Read the full file on GitHub · 282 lines

Files

What ships with it

3 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.

2mo ago First seen · 282 lines · 133 tokens per session scan A d3b082f2a001

Subscribe to this mod's changes

boltz is a skill published in the GitHub repository naity/FM4Life (2 stars, last pushed 7mo ago), licensed MIT. It adds 133 tokens to every session and 2,467 once invoked, about $0.0005 per session on Opus 5.5. 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 2026-08-31.

Scientific agent-skills ai-agents alphafold bioinformatics computational-biology drug-discovery

boltz next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
boltznaity/FM4Life	Skill	2	7mo ago	MIT	A	133	Claude Code, Codex
statistical-modelinginflexa-ai/inflexa	Skill	36	yesterday	Apache-2.0	A	26	Claude Code, Codex
genomic-variantsinflexa-ai/inflexa	Skill	36	yesterday	Apache-2.0	A	31	Claude Code, Codex
bulk-transcriptomicsinflexa-ai/inflexa	Skill	36	yesterday	Apache-2.0	A	26	Claude Code, Codex
chromatin-regulationinflexa-ai/inflexa	Skill	36	yesterday	Apache-2.0	A	32	Claude Code, Codex
spatial-omicsinflexa-ai/inflexa	Skill	36	yesterday	Apache-2.0	A	28	Claude Code, Codex
drug-repurposinginflexa-ai/inflexa	Skill	36	yesterday	Apache-2.0	A	30	Claude Code, Codex