🔥 BondForge v1.0.0 - Forging the Future of Protein Analysis

🔥 BondForge v1.0.0 - Initial Public Release

Forging Insights from Chemical Bonds

We're excited to announce the first stable release of BondForge! 🎉

What is BondForge?

BondForge is the most comprehensive open-source toolkit for analyzing protein-protein interactions. While other tools focus on small molecules or offer limited interaction detection, BondForge provides complete, automated analysis with unmatched depth.

---

✨ Key Features

🔬 Comprehensive Interaction Detection

• 20 interaction types - more than any free tool
• Hydrogen bonds, salt bridges, disulfide bonds
• Hydrophobic, π-π stacking, cation-π, halogen bonds
• Van der Waals, anion-π, sulfur-aromatic, CH-π
• Metal coordination and more!

🕸️ Advanced Network Analysis

• Hub residue identification
• Critical interaction paths
• Protein interaction networks
• Interface characterization

🎯 Protein-Protein Focus

• Designed for protein complexes
• Interface hotspot detection
• Binding site analysis
• Stability assessment

🎨 Publication-Ready Output

• High-resolution network graphs
• PyMOL visualization scripts
• CSV data exports
• Statistical summaries

---

🚀 Quick Start

# Clone and install
git clone https://github.com/AyehBlk/BondForge.git
cd BondForge
pip install -r requirements.txt
pip install -e .

# Basic usage
from src.extended_interaction_analyzer import ExtendedProteinInteractionAnalyzer

forge = ExtendedProteinInteractionAnalyzer('protein.pdb')
results = forge.analyze_all_interactions()
hubs = forge.identify_hubs()

---

📊 What Makes BondForge Unique?

Feature	BondForge	Others
Interaction Types	20	5-8
Protein-Protein	✅	⚠️
Network Analysis	✅	❌
Open Source	✅	Varies
Cost	FREE	$0-50k

---

📚 Documentation

• Quick Start: QUICKSTART.md
• Full Docs: docs/
• Examples: examples/

---

🎯 Perfect For

• 🧬 Antibody engineering
• 💊 Drug discovery
• 🔧 Protein engineering
• 📊 Structural biology
• 🏭 Bioinformatics pipelines

---

📝 Citation

@software{bondforge2025,
  author    = {Ayeh Bolouki},
  title     = {BondForge: Forging Insights from Chemical Bonds},
  year      = 2025,
  version   = {1.0.0},
  publisher = {Zenodo},
  url       = {https://github.com/AyehBlk/BondForge}
}

---

🤝 Contributing

We welcome contributions! See CONTRIBUTING.md

---

📞 Support

• 📧 Email: ayehbolouki1988@gmail.com (general inquiries)
• 📧 Consulting: ayehgeek@gmail.com
• 💬 Discussions
• 🐛 Issues

---

📄 License

MIT License - Free for academic and commercial use.

---

🔥 Happy forging! 🔥

BondForge v1.0.0 - November 5, 2025