alphafold2 SKILL.md skillA
alphafold2 from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/alphafold2@git:20260828.e9753bePins git:20260828.e9753be in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/alphafold2/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260828.e9753be, committed Aug 28, 2026
- First version recorded
- Jul 6, 2026
- Size
- 5,062 bytes
- Repository stars
- 662
- License
- MIT
Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022, github.com/sokrypton/ColabFold; AlphaFold2 Jumper et al. 2021). Reach for this skill to fold a sequence or complex with the AF2/AF2-Multimer evoformer, to validate designed sequences by self-consistency pLDDT, ipTM, and RMSD, or to run a quick MSA-backed prediction using the public MMseqs2 server.
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
# AlphaFold2 (ColabFold runner) This skill wraps AlphaFold2 and AlphaFold2-Multimer through `colabfold_batch`, which replaces DeepMind's local-database MSA pipeline with a call to the public MMseqs2 server — so a prediction is one command and one FASTA, not a 2 TB database mount. AF2 remains the reference monomer predictor and the multimer model is still a strong protein–protein validator, but it does not handle ligands or nucleic acids; for those, route to `boltz`, `chai1`, or `openfold3`. The ColabFold code is MIT (github.com/sokrypton/ColabFold) and the AlphaFold2 code is Apache-2.0 (github.com/google-deepmind/alphafold); the AF2 model parameters are CC-BY-4.0 with DeepMind's terms of use. ## Running it ```bash colabfold_batch input.fasta out \ --num-recycle 3 \ --model-type alphafold2_multimer_v3 ``` The input is a plain FASTA. For a complex, put every chain on one sequence line separated by `:` — `colabfold_batch` builds a paired MSA per segment and runs the multimer model when it sees the colon (so the explicit `--model-type alphafold2_multimer_v3` above is belt-and-braces). For monomers omit `--model-type` and the colon. `--templates` and `--amber` add PDB templates …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/alphafold2@sha256:137f4859c1ae250bThe line at the top of this page pins the label git:20260828.e9753be, 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_6553p46hp7zfq3gu)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Jul 6, 2026 and Aug 28, 2026, about one every 53 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260828.e9753be latest | 2026-08-28 | e9753be | 5,062 B | A | view · diff |
| git:20260706.f35863d | 2026-07-06 | f35863d | 4,998 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 (5062 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
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_6553p46hp7zfq3gu GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/alphafold2 GET https://markdownregistry.com/api/v1/blob/137f4859c1ae250b5c8150f69eec96ec66e7c57ff5b314fad2688ad76eed0404
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.
More from pku-yuangroup/openai4s
Every file in pku-yuangroup/openai4s