DockSuiteX

All-in-one Protein-Ligand Docking Package

DockSuiteX is a comprehensive Python package and GUI application for molecular docking that integrates multiple tools including MGLTools, P2Rank, AutoDock Vina, and AutoDock4. It provides a unified, user-friendly interface for protein and ligand preparation, binding pocket prediction, and molecular docking simulations — available both as a Python package and an easy-to-use GUI.

✨ Key Features

• 🔧 Automated Preparation: Streamlined protein and ligand preparation using PDBFixer and Open Babel
• 🎯 Pocket Prediction: Binding pocket prediction with P2Rank machine learning
• ⚡ Multiple Docking Engines: Support for both AutoDock Vina and AutoDock4
• 📊 Batch Processing: High-throughput screening with parallel execution
• 👁️ Interactive Visualization: 3D molecular visualization with NGLView
• 🔍 Interaction Profiling: Post-docking interaction fingerprinting with ProLIF
• 🌐 Molecule Fetching: Fetch structures from RCSB PDB, PubChem, and ChEMBL
• 🧩 Format Conversion: Convert molecular file formats locally with Open Babel
• 🧪 MolSynthAI: Generate structurally similar molecules for docking & lead optimization — powered by AI
• 🖥️ Interactive GUI: Complete GUI application — no coding required

🚀 Flexible Batch Docking

DockSuiteX is uniquely designed to handle ALL possible docking combinations, making it the most versatile docking package for high-throughput screening. Whether you're working with a single molecule or thousands, DockSuiteX adapts to your needs:

✅ 1 Ligand → 1 Receptor Standard molecular docking for detailed interaction analysis

✅ Many Ligands → 1 Receptor Virtual screening - screen compound libraries against a single protein target

✅ 1 Ligand → Many Receptors Inverse docking - test one compound against multiple protein variants or different targets

✅ Many Ligands → Many Receptors Complete combinatorial screening - explore all possible ligand-receptor interactions in one run

All batch operations leverage parallel execution to maximize computational efficiency, enabling high-throughput virtual screening on your local machine without requiring cluster computing resources.

🖥️ GUI Application

DockSuiteX includes a full-featured GUI application built with Streamlit, providing a graphical interface for all docking workflows — no coding required. Simply run docksuitex in your terminal to launch the app.

GUI Pages:

• 🏠 Home — Landing page with feature overview and docking scenario cards
• 🔬 Single Docking — Complete workflow: upload molecules, prepare structures, find binding pockets, configure & run docking, visualize results in 3D
• ⚡ Batch Docking — High-throughput screening with parallel execution for all ligand-receptor combinations
• 🌐 Fetch Molecules — Download protein (PDB) and ligand (SDF) structures directly from RCSB PDB, PubChem, and ChEMBL
• 🧩 Format Converter — Convert molecular file formats using Open Babel
• 🧪 MolSynthAI — Generate structurally similar molecules for docking & lead optimization — powered by AI
• 📌 About — Citations, references, and contributing information

📚 Documentation

📖 For complete documentation, API reference, and examples, visit:

https://mangalamgsinha.github.io/DockSuiteX/

📦 Quick Install

pip install docksuitex

After installation, you can launch the application by simply typing:

docksuitex

If the command is not recognized, try:

python -m docksuitex

Requirements: Python 3.9+, Windows OS

📜 License

GNU GPL v3 - see LICENSE for details.

🙏 Acknowledgments

This package builds upon and automates workflows using:

• AutoDock4 & AutoDock Vina
• MGLTools
• Open Babel
• PDBFixer
• P2Rank
• RCSB PDB & PubChem
• NGLView
• ProLIF