🧬 Protein Structure-Function Analysis Tool

Live Application: https://protein-hmm-app-production.up.railway.app 🚀

A sophisticated web application for analyzing protein secondary structure and understanding structure-function relationships using advanced computational biology algorithms.

🎯 What This App Does

Transform any protein sequence into detailed structural and functional insights in seconds! This tool bridges the gap between protein sequence and biological function by:

• 🔬 Predicting 8-state secondary structure using the enhanced Chou-Fasman method
• 🎯 Identifying functional regions and their biological roles
• 🧪 Analyzing binding potential and active sites
• 📊 Providing flexibility analysis for protein dynamics
• 🏗️ Detecting structural motifs like helix-turn-helix and beta hairpins
• 📚 Educational content about structure-function relationships

✨ Key Features

🔬 Advanced Secondary Structure Prediction

• 8-state DSSP classification: H (α-helix), G (3₁₀-helix), I (π-helix), E (β-strand), B (β-bridge), T (turn), S (bend), C (coil)
• Enhanced Chou-Fasman algorithm with contextual analysis
• 60-65% prediction accuracy with confidence scoring
• Color-coded visualization for easy interpretation

🎯 Structure-Function Relationship Analysis

• Functional region identification with biological explanations
• Binding site prediction based on flexibility and structural context
• Motif detection for common functional patterns
• Flexibility profiling showing rigid vs. dynamic regions

📊 Comprehensive Results Dashboard

• Interactive sequence visualization with structure mapping
• Statistical composition analysis (helical, extended, coil content)
• Detailed residue-by-residue breakdown
• Professional scientific presentation

🚀 User-Friendly Interface

• Single sequence analysis with instant results
• Batch processing for multiple sequences (up to 50)
• Example proteins (insulin, lysozyme, myoglobin)
• Educational modules explaining the science
• Mobile-responsive design

🧪 How to Use

Quick Start

1. Visit: https://protein-hmm-app-production.up.railway.app
2. Paste your protein sequence (amino acids only: ACDEFGHIKLMNPQRSTVWY)
3. Click "Analyze Structure & Function"
4. Explore the results!

Input Formats

• Raw sequence: MKWVTFISLLLLFSSAYSRGVFR...
• FASTA format (for batch analysis):

  >Protein1
  MKWVTFISLLLLFSSAYSRGVFR
  >Protein2
  RDTHKSEIAHRFKDLGEEHFKG
  

Example Analyses

Try these example proteins to see the tool in action:

🍯 Insulin (Hormone)

GIVEQCCTSICSLYQLENYCN

Small hormone with predominantly helical structure

🦠 Lysozyme (Enzyme)

KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL

Antimicrobial enzyme with mixed α/β structure

🫁 Myoglobin (Oxygen Storage)

VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG

All-alpha oxygen storage protein

🔬 The Science Behind It

Chou-Fasman Method

Our enhanced implementation of the classic Chou-Fasman algorithm uses:

• Amino acid propensities for different secondary structures
• Local context analysis with sliding windows
• Post-processing rules for realistic structure assignment
• 8-state DSSP mapping for detailed classification

Structure-Function Analysis

The tool identifies how structure drives function through:

• Helical regions: Often involved in stability and binding
• β-strands: Critical for enzyme active sites and interfaces
• Flexible loops: Frequently contain regulatory and binding sites
• Turns and bends: Important for protein dynamics and allosteric changes

Biological Relevance

Understanding protein structure-function relationships is crucial for:

• Drug design: Identifying binding sites and conformational changes
• Protein engineering: Modifying function through structural changes
• Disease research: Understanding how mutations affect protein function
• Evolutionary biology: Analyzing conservation of functional elements

📊 Understanding Your Results

Secondary Structure Colors

• 🔴 Red: α-helix (H), 3₁₀-helix (G), π-helix (I)
• 🔵 Blue: β-strand (E), β-bridge (B)
• 🟢 Green: Turn (T), Bend (S)
• ⚫ Gray: Coil/Loop (C)

Functional Implications

• Helical regions: Structural stability, protein-protein interactions
• Extended regions: Enzyme active sites, β-sheet formation
• Flexible regions: Binding sites, regulatory elements, allosteric sites
• Turn regions: Conformational flexibility, surface loops

Confidence Scores

• >80%: High confidence prediction
• 60-80%: Good confidence prediction
• <60%: Lower confidence, consider experimental validation

🛠️ Technical Details

Built With

• Backend: Python 3.11+ with Flask
• Frontend: Modern HTML5, CSS3, JavaScript
• Algorithms: Enhanced Chou-Fasman method
• Deployment: Railway platform
• Architecture: RESTful API design

API Endpoints

POST /api/predict_structure_function
POST /api/analyze_batch
GET  /api/get_educational_content

Dependencies

flask>=2.3.0
flask-cors>=4.0.0
numpy>=1.24.0

🚀 Deployment

This application is deployed on Railway with automatic deployments from GitHub.

Deploy Your Own Instance

1. Fork this repository
2. Connect to Railway: https://railway.app
3. Deploy from GitHub
4. Your app goes live automatically!

Local Development

git clone https://github.com/LDolanLDolan/protein-hmm-app.git
cd protein-hmm-app
pip install -r requirements.txt
python app.py

📈 Future Enhancements

Planned Features

• 🧠 Machine Learning Models: Deep learning for higher accuracy
• 🧬 3D Structure Visualization: Interactive molecular graphics
• 📊 Advanced Analytics: Phylogenetic analysis, domain architecture
• 🔄 Real-time Collaboration: Share and discuss results
• 📱 Mobile App: Native iOS/Android applications

Scientific Improvements

• Training on PDB data: Real experimental structures
• Ensemble methods: Combining multiple prediction algorithms
• Homology modeling: 3D structure prediction
• Functional annotation: GO terms and pathway analysis

🎓 Educational Use

Perfect for:

• Bioinformatics courses: Hands-on protein analysis
• Structural biology classes: Understanding secondary structure
• Research training: Learning computational biology tools
• Self-study: Interactive learning about proteins

🤝 Contributing

We welcome contributions! Areas for improvement:

• Algorithm enhancements: Better prediction methods
• UI/UX improvements: Enhanced user experience
• Educational content: More learning modules
• Performance optimization: Faster analysis
• Testing: Comprehensive test coverage

📄 License

This project is open source and available under the MIT License.

👥 Authors

LDolanLDolan - Initial work and development

🙏 Acknowledgments

• Chou & Fasman: Original secondary structure prediction method
• DSSP: Defining secondary structure classification
• Railway: Excellent deployment platform
• Open source community: Tools and libraries that made this possible

📞 Support

• 🌐 Live App: https://protein-hmm-app-production.up.railway.app
• 🐛 Issues: GitHub Issues
• 💬 Discussions: GitHub Discussions

---

Try it now: https://protein-hmm-app-production.up.railway.app 🚀

Transforming protein sequences into biological insights, one analysis at a time. 🧬✨