smina (Claude Skill)

Smina molecular docking CLI.

   
Type Claude Skill
Supplier jaechang-hits (community OSS, CC BY 4.0)
Availability GA — part of the BixBench-evaluated SciAgent-Skills collection
Pricing Free / OSS (GPL-2.0)
Capabilities Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

SciAgent-Skills is not an npm package — skills are plain markdown read directly by the agent (no npx/npm).

  • Claude Code — clone and load as a plugin: 
    git clone https://github.com/jaechang-hits/SciAgent-Skills

    Then inside Claude Code run /plugin install sciagent-skills (verify it appears under /plugin → Installed). Clone into your project directory so Claude Code picks the skills up via CLAUDE.md.

  • Manual / other agents — point the agent at the skill file directly: 
    cp -r SciAgent-Skills/skills/structural-biology-drug-discovery/smina-molecular-docking ~/.claude/skills/

    The skill declares its own Python dependencies in its SKILL.md; install them when prompted on first use.

What it does

smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score breakdowns. Pipeline: receptor PDBQT prep -> ligand prep (RDKit/OpenBabel) -> dock via autobox or explicit grid -> rescore/minimize with custom scoring -> rank poses by affinity. Choose smina over Vina when you need custom scoring terms (–custom_scoring), local optimization of an existing pose (–local_only), per-atom contributions (–atom_term_data), or SDF/MOL2 ligands without manual PDBQT conversion. For unknown binding sites use diffdock; for the Python-bindings/Vinardo workflow use autodock-vina-docking.

Primary use cases: Smina molecular docking CLI.

Notes

Distributed as a SKILL.md (plus code examples) in the SciAgent-Skills collection — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: GPL-2.0. The skill directory upstream is skills/structural-biology-drug-discovery/smina-molecular-docking.

Sources

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