boltz SKILL.md skillA
boltz from aipoch/open-science is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add aipoch/open-science/boltz@git:20260814.c9a70d8Pins git:20260814.c9a70d8 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- aipoch/open-science
- Path
resources/skills/boltz/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260814.c9a70d8, committed Aug 14, 2026
- First version recorded
- Jul 14, 2026
- Size
- 5,687 bytes
- Repository stars
- 5,279
- License
- Apache-2.0
Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. 2025, github.com/jwohlwend/boltz). Reach for this skill to validate designed binders against a target, to co-fold a protein with a SMILES or CCD ligand, or to get an open-source AlphaFold3 alternative with optional binding-affinity prediction.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Boltz-2
Boltz-2 is the open-weights diffusion co-folder closest in surface to
AlphaFold3: a YAML describing protein, DNA, RNA, and ligand chains in, mmCIF
plus pTM/ipTM/pLDDT confidences out, with an optional small-molecule affinity
head. Among our four co-fold skills it is the default for binder-validation
campaigns — fully open MIT weights and the fastest sampler; pick `chai1` when
you want a second independent model for consensus, `openfold3` when AF3-faithful
settings matter, and `esmfold2` when you can live without an MSA. Code and
weights are MIT (PyPI `boltz`, github.com/jwohlwend/boltz).
## Running it
```yaml
# complex.yaml
version: 1
sequences:
- protein:
id: A
sequence: MVTPEGNVSLVDESLLVGVTDEDRAVRS... # target
- protein:
id: B
sequence: AIQRTPKIQVYSRHPAENG... # binder
- ligand:
id: L
smiles: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O' # or ccd: SAH
```
```bash
boltz predict complex.yaml \
--use_msa_server --out_dir out/ --recycling_steps 3 --diffusion_samples 5
```
Each protein chain needs an MSA; without one the run exits before the model
loads. `--use_msa_server` queries `api.colabfold.com` (expect a 30–90 s pause
…Read the whole file at its exact version.
How to install
mdr add aipoch/open-science/boltz@sha256:3971ac101972455dThe line at the top of this page pins the label git:20260814.c9a70d8, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_rk4dytowbai5abl6)
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Versions
The registry has recorded 2 versions of this file, between Jul 14, 2026 and Aug 14, 2026, about one every 31 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260814.c9a70d8 latest | 2026-08-14 | c9a70d8 | 5,687 B | A | view · diff |
| git:20260714.a2a3282 | 2026-07-14 | a2a3282 | 5,305 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (5687 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
aipoch/open-science · 5,279 stars · license Apache-2.0 · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_rk4dytowbai5abl6 GET https://markdownregistry.com/api/v1/resolve?ref=aipoch/open-science/boltz GET https://markdownregistry.com/api/v1/blob/3971ac101972455d8c92fba4fb950da05d65f4781634bf6bd06d99976b711584
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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