🧬 PyMOL Plugin for Molecular Glue Discovery & Analysis

Features • Installation • Quick Start • Tutorials • Documentation

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📖 Overview

GLINT is a comprehensive PyMOL plugin designed for molecular glue discovery and protein-ligand interaction analysis. It provides specialized tools for analyzing ternary complexes, detecting G-motifs, identifying neo-epitopes, and structure-guided optimization workflows.

🔬 What are Molecular Glues?

Molecular glues are small molecules that induce or stabilize protein-protein interactions, typically between an E3 ubiquitin ligase and a target protein (neo-substrate), leading to targeted protein degradation.

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✨ Features

🎯 Target Discovery G-Motif Detection - CRBN G-loop binding motifs via RMSD matching Protein Surface Analysis - Electrostatic and hydrophobic patch analysis Surface Similarity & Complementarity - Surface-based comparison with APBS-supported electrostatics

🔍 Hit Identification Vina Docking - Integrated AutoDock Vina HADDOCK3 Integration - Ternary complex modeling FoldX Mutation Analysis - Mutational binding energy prediction

🧩 Ternary Complex Evaluation Automated Ternary Complex Analysis - One-click full evaluation with automatic ligand property calculation Comprehensive Interface Analysis - BSA calculation using ternary complex formula, contact statistics Ligand Property Extraction - Automatic SMILES extraction and molecular property computation (MW, LogP, TPSA, etc.) Geometric Metrics - COG shift, E3-MG-POI angle, distance measurements, duality index Enhanced CSV Export - Consistent with GUI display, includes timestamps and detailed results

⚡ Lead Optimization Electrostatic Complementarity Analysis - Ligand and ternary EC analysis workflows PPI Interface Analysis - Interaction type classification Protein-Ligand Interactions - H-bonds, salt bridges, π-π, etc.

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📦 Installation

🍎 macOS Installer (Recommended)

1. Download GLINT_Installer_0.3.0.dmg from Releases
2. Open the DMG and run the installer
3. Follow the on-screen instructions

🚀 One-Shot Setup Script

bash install_glint.sh

🪟 Windows Installation

1. Download GLINT_Installer_X.X.X.exe from Releases
2. Double-click the .exe file and follow the installation wizard
3. Restart PyMOL to load the plugin

🐧 Linux Installation

chmod +x install_glint.sh
./install_glint.sh

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🚀 Quick Start

1. Launch PyMOL and load your protein structure
2. Access GLINT Menu - Look for the "GLINT" menu in the menu bar
3. Run Analysis - Navigate to the desired analysis tool
4. View Results - Results are displayed in real-time with visualization options

Example: Ternary Complex Evaluation

# Load your ternary complex structure
load ternary_complex.pdb

# Access GLINT -> Ternary Complex Evaluation
# Set parameters:
# - E3 Chain: A
# - POI Chain: B  
# - Ligand Resn: UNL

# Click "Run Full Evaluation"
# GLINT will automatically:
# - Calculate interface BSA using ternary complex formula
# - Extract ligand SMILES and compute molecular properties
# - Analyze geometric metrics (COG shift, angles, distances)
# - Calculate duality index for binding balance

# Export results via "Export" button

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📚 Documentation

• Installation Guide - Detailed installation instructions
• Tutorial - Step-by-step tutorials for all features
• API Reference - Complete API documentation

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🎯 Key Features in v0.3.0

✨ New: Automated Ternary Complex Analysis

• One-click full evaluation - Run complete analysis with single button click
• Automatic ligand property calculation - SMILES extraction and molecular computation
• Enhanced BSA calculation - Using ternary complex formula with intermediate values
• Improved CSV export - Consistent with GUI display, includes timestamps

🔧 Improvements

• Better error handling and user feedback
• Real-time progress updates
• Enhanced visualization options
• Improved documentation and tutorials

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🤝 Contributing

We welcome contributions! Please see our Contributing Guidelines for details.

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📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

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🙏 Acknowledgments

• PyMOL community for the excellent molecular visualization platform
• RDKit and OpenBabel for chemical informatics tools
• BioPython for structural biology utilities
• All contributors and users of GLINT

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Made with ❤️ by the GLINT Team