bio-alignment-structural skillA
bio-alignment-structural is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
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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` …
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How to install
mdr add pku-yuangroup/openai4s/bio-alignment-structural@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-structural@sha256:e3ddefc217da1edaPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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