Individual skill
bio-alignment-structural
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.
skills/bioskills/bio-alignment-structural-alignment/SKILL.md
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## 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`