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bio-structural-biology-structure-preparation

82 / 100 · Low risk

Fine to try.

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

Prepares a deposited or predicted structure for docking, molecular dynamics, or electrostatics by adding hydrogens, assigning protonation and tautomer states, and filling missing atoms and short loops with PDBFixer, reduce, PROPKA, and PDB2PQR. Use when adding hydrogens an X-ray model never resolved; assigning His HID/HIE/HIP tautomers, Asn/Gln/His 180-degree flips, and Cys/Lys/Asp/Glu pKa-shifted protonation at a stated pH and microenvironment rather than trusting standard pKa 7; filling missi…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

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

if [ -e ~/.agents/skills/'bio-structural-biology-structure-preparation' ] || [ -L ~/.agents/skills/'bio-structural-biology-structure-preparation' ]; then echo 'A skill folder named bio-structural-biology-structure-preparation 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-structural-biology-structure-preparation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-structural-biology-structure-preparation' ~/.agents/skills/'bio-structural-biology-structure-preparation' && 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-structural-biology-structure-preparation' ~/.claude/skills/'bio-structural-biology-structure-preparation' (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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