bio-alignment-structural

80 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

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.

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

The author does not mention this.

Found in 11 places.

skills/bio-alignment-structural/SKILL.md, line 96TMalign chainA.pdb chainB.pdb -o superposed.sup
skills/bio-alignment-structural/SKILL.md, line 117foldseek easy-multimersearch query_complex.pdb afdb_multimer result tmp/
skills/bio-alignment-structural/SKILL.md, line 156foldseek easy-search query.pdb afdb_database result.m8 tmp/

Show 8 more

skills/bio-alignment-structural/SKILL.md, line 183foldseek createdb --mask-bfactor-threshold 70.0 *.pdb afdb_masked
skills/bio-alignment-structural/SKILL.md, line 199foldmason easy-msa structures/*.pdb result tmp/ \
skills/bio-alignment-structural/SKILL.md, line 211foldmason easy-msa structures/*.pdb result tmp/ --report-mode 2
skills/bio-alignment-structural/SKILL.md, line 233t_coffee input.fasta -mode expresso -output fasta_aln -outfile aligned.fasta
skills/bio-alignment-structural/SKILL.md, line 271pymol -cq -d "load reference.pdb; load mobile.pdb; super mobile, reference; ray 800,600; png fig.png"
skills/bio-alignment-structural/examples/foldmason_msa.py, line 22subprocess.run(cmd, check=True)
skills/bio-alignment-structural/examples/foldseek_search.py, line 21subprocess.run(cmd, check=True)
skills/bio-alignment-structural/examples/tm_align_pairwise.py, line 18result = subprocess.run(cmd, capture_output=True, text=True, check=True)

Downloads and installs other software

The author does not mention this.

Found in 2 places.

skills/bio-alignment-structural/usage-guide.md, line 19pip install biopython
skills/bio-alignment-structural/usage-guide.md, line 22pip install fair-esm # ESM-2 embeddings

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-alignment-structural' ] || [ -L ~/.agents/skills/'bio-alignment-structural' ]; then echo 'A skill folder named bio-alignment-structural already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-alignment-structural' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-alignment-structural' ~/.agents/skills/'bio-alignment-structural' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-alignment-structural' ~/.claude/skills/'bio-alignment-structural' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-11	`908229c`	80