bio-alignment-structural SKILL.md skillA
bio-alignment-structural 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/bio-alignment-structural@git:20260821.2d1b678Pins git:20260821.2d1b678 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/bioskills/bio-alignment-structural-alignment/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 23,783 bytes
- Repository stars
- 662
- License
- MIT
Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.
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
## Version Compatibility Reference examples tested with: Foldseek 8+, TM-align 20220412+, US-align 20231222+, Foldmason 1+, BioPython 1.83+, pymol-open-source 3.0+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `foldseek --version`, `TMalign`, `USalign`, `foldmason --version` - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Structural Alignment **"Align two protein structures"** -> Compute backbone-aware superposition and a fold-similarity score (TM-score, RMSD, or LDDT). - CLI pairwise: `TMalign A.pdb B.pdb`, `USalign A.pdb B.pdb` - CLI search at scale: `foldseek easy-search query/ AFDB result.m8 tmp/` - CLI structural MSA: `foldmason easy-msa structures/*.pdb out tmp/` - Python pairwise: `Bio.PDB.Superimposer`, or `subprocess` wrapping `TMalign` / `USalign` (see `examples/tm_align_pairwise.py`) - GUI / scripted molecular-graphics superposition: ChimeraX `matchmaker`, PyMOL `super`/`cealign` …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-alignment-structural@sha256:e3ddefc217da1edaThe line at the top of this page pins the label git:20260821.2d1b678, 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_76k2r4s32g7f5tba)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_76k2r4s32g7f5tba GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-alignment-structural GET https://markdownregistry.com/api/v1/blob/e3ddefc217da1edafe020e9855b428d73caa99065722ee2ea40323138c47ce40
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.