Agent 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.

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeships scriptsNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill structural-alignment --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 6
SKILL.md size: 23 KB
Bundled scripts: yes
Path: skills/bioskills/structural-alignment/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the SKILL.md

## 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` **"Find structural homologs of an AlphaFold model"** → Search

What's inside
Steps it walks through
  1. Version Compatibility
  2. When to Use Structural Alignment
  3. Twilight-Zone Threshold Exceptions
  4. Pairwise Structural Alignment Tool Selection
  5. Foldseek vs DALI: Modern Comparison
  6. TM-score Threshold Caveats
  7. TM-align Pairwise Run
  8. Foldseek-Multimer for Database-Scale Complex Search
  9. Bio.PDB.Superimposer
  10. Structural Search at Scale: Foldseek
  11. pLDDT-Filtering AlphaFold Structures Before Foldseek
  12. Structural Multiple Sequence Alignment
  13. Foldmason easy-msa
  14. Hybrid Sequence-Structure Approaches
Ships with 5 files
  • examples/biopython_superimposer.py
  • examples/foldmason_msa.py
  • examples/foldseek_search.py
  • examples/tm_align_pairwise.py
  • usage-guide.md
Commands it runs
TMalign chainA.pdb chainB.pdb -o superposed.sup
TMalign chainA.pdb chainB.pdb -outfmt 2
USalign chainA.pdb chainB.pdb -mol prot -outfmt 2
USalign complex_A.pdb complex_B.pdb -mm 1 -ter 0
foldseek easy-multimersearch query_complex.pdb afdb_multimer result tmp/
foldseek easy-multimersearch query_complex.pdb afdb_multimer result tmp/ --multimer-tm-threshold 0.5
foldseek easy-multimercluster *.pdb cluster_result tmp/ --multimer-tm-threshold 0.65
Search query structures against AFDB (default: --alignment-type 2)
foldseek easy-search query.pdb afdb_database result.m8 tmp/
Refine top hits with full TM-align rotation (slower but global TM-score)
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About this skill
What does the bio-alignment-structural skill do?

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.

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill structural-alignment --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.

Where does this skill come from?

From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.

Is a popular skill a good skill?

Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.

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