protein-docking-configurator

name	protein-docking-configurator
description	Prepare input files for molecular docking software, automatically determine Grid Box center and size. Supports AutoDock Vina, AutoDock4, and other mainstream docking tools.
version	1.0.0
category	Bioinfo
tags	[]
author	AIPOCH
license	MIT
status	Draft
risk_level	Medium
skill_type	Tool/Script
owner	AIPOCH
reviewer
last_updated	2026-02-06

Protein Docking Configurator

Features

• Parse protein PDB files, identify ligand binding pockets
• Automatically calculate Grid Box center coordinates and dimensions
• Generate AutoDock Vina configuration files
• Generate AutoDock4 Grid parameter files
• Support Box positioning based on active site residues or ligands

Usage

As Command Line Tool

# Calculate Grid Box based on active site residues
python scripts/main.py --receptor protein.pdb --active-site-residues "A:120,A:145,A:189" --software vina

# Calculate Grid Box based on reference ligand
python scripts/main.py --receptor protein.pdb --reference-ligand ligand.pdb --software vina

# Manually specify Box parameters
python scripts/main.py --receptor protein.pdb --center-x 10.5 --center-y -5.2 --center-z 20.1 --size-x 20 --size-y 20 --size-z 20 --software vina

As Python Module

from scripts.main import DockingConfigurator

config = DockingConfigurator()

# Calculate box from receptor and active site
config.from_active_site("protein.pdb", ["A:120", "A:145", "A:189"])
config.write_vina_config("config.txt", exhaustiveness=32)

# Calculate box from receptor and reference ligand
config.from_reference_ligand("protein.pdb", "ligand.pdb", padding=5.0)
config.write_autodock4_gpf("protein.gpf", spacing=0.375)

Parameter Description

Command Line Parameters

Parameter	Description	Required
--receptor	Receptor protein PDB file path	Yes
--software	Docking software type (vina/autodock4)	Yes
--active-site-residues