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protein-docking-lightdock

80 / 100 · Low risk

Fine to try.

By ssinder/bioinformatics-agent-skills (GitHub) · research · 75 stars · scanned at commit 42cf1a9

Runs LightDock protein-protein docking locally by driving the lightdock3_setup.py and lightdock3.py executables, then extracts the best docked complex. Parses the GSO swarm output files with the correct field semantics (glowworm id is the line number, not the LigID column), selects the latest gso_<step>.out by numeric step rather than dictionary order, and generates conformations from the origin-shifted structures that the setup stage produced so the receptor and ligand stay in a consistent coo…

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/'protein-docking-lightdock' ] || [ -L ~/.agents/skills/'protein-docking-lightdock' ]; then echo 'A skill folder named protein-docking-lightdock already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/ssinder/bioinformatics-agent-skills' "$d" && git -C "$d" checkout --quiet '42cf1a9c2381b25047dae98ca944ee7b52781ed8' -- 'skills/protein-docking-lightdock' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/protein-docking-lightdock' ~/.agents/skills/'protein-docking-lightdock' && 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/'protein-docking-lightdock' ~/.claude/skills/'protein-docking-lightdock' (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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