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foldseek-structural-search

100 / 100 · Low risk

Fine to try.

By mkurman/zorai (GitHub) · coding · 327 stars · scanned at commit 8ea1fc3

Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.

Works with any agent that supports SKILL.md skills.

What this skill can do

We found nothing in the files we read that matches our rules. That does not prove the skill is safe: see the limits of static scanning.

Install

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

if [ -e ~/.agents/skills/'foldseek-structural-search' ] || [ -L ~/.agents/skills/'foldseek-structural-search' ]; then echo 'A skill folder named foldseek-structural-search already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/mkurman/zorai' "$d" && git -C "$d" checkout --quiet '8ea1fc3ae126b6e103b8508bacd8f5aa60b6f4ad' -- 'skills/scientific-skills-gdm/foldseek_structural_search' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/scientific-skills-gdm/foldseek_structural_search' ~/.agents/skills/'foldseek-structural-search' && 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/'foldseek-structural-search' ~/.claude/skills/'foldseek-structural-search' (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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