smina Molecular Docking

smina Molecular Docking

Overview

smina is an AutoDock Vina 1.1.2 fork focused on flexible scoring and minimization. Accepts SDF/MOL2/PDB ligands directly (no manual PDBQT), autoboxes from a reference ligand, ships six built-in scoring functions plus arbitrary --custom_scoring terms, and prints per-atom score contributions. CLI-only — drive from Python via subprocess.

When to Use

• Re-scoring or locally minimizing an existing pose (--local_only, --minimize) without a full search
• Single-pose binding energy without docking (--score_only)
• Docking with a custom or empirical scoring function tuned to a target class
• SDF/MOL2/multi-ligand input without per-ligand PDBQT conversion
• Autoboxing the grid around a co-crystallized reference ligand
• Per-atom energy decomposition (--atom_term_data) for medchem analog design
• Batch virtual screening that parallelizes well across nodes (one CLI process per ligand)
• Use autodock-vina-docking instead when you need Vina Python bindings, Vinardo scoring, or Vina 1.2's expanded force field; use diffdock when the binding site is unknown

Prerequisites

• smina binary — conda-forge or SourceForge build
• Python: rdkit, openbabel-wheel (or system openbabel), prody, pandas, py3Dmol
• ADFR Suite for prepare_receptor (receptor PDBQT only — ligands handled by smina)
• Data: protein (PDB / PDB ID), ligand(s) as SMILES / SDF / MOL2

Check before installing — inside a pixi/conda env smina is usually already on PATH. If command -v smina succeeds, skip install; inside a pixi project invoke as pixi run smina ....

command -v smina || conda install -c conda-forge smina openbabel
pip install rdkit prody pandas py3Dmol
# ADFR Suite: https://ccsb.scripps.edu/adfr/downloads/

Quick Start

End-to-end docking using autobox from a reference ligand:

import subprocess

result = subprocess.run([