🧬 BioAI Protein Modeling

A learning project focused on protein modeling and BioAI, building towards expertise in computational biology and AI-driven protein analysis.

📋 About

This repository contains my journey learning protein modeling and BioAI, with the goal of becoming a strong candidate for companies like EvolutionaryScale. The project focuses on:

• FASTA sequence analysis - Reading and processing protein sequences
• Protein mutations - Generating and analyzing point mutations
• ESM embeddings - Using Meta's Evolutionary Scale Modeling for protein representations
• RESTful API - Building a FastAPI service for protein analysis

🛠️ Technologies

• Python 3.12+
• Biopython - Biological sequence manipulation
• Jupyter Notebooks - Interactive experimentation
• FastAPI - Modern web framework for APIs
• ESM Models - Pre-trained protein language models (Meta AI)

📁 Project Structure

bioai-protein-modeling/
├── src/
│   ├── data/           # FASTA file utilities
│   ├── mutations/      # Protein mutation tools
│   ├── embeddings/     # ESM embedding generation
│   └── api/            # FastAPI REST service
├── notebooks/
│   ├── week1/          # Week 1 experiments
│   └── week2/          # Week 2 experiments
└── reports/            # Weekly progress reports

🚀 Roadmap

• Initial project structure
• Basic FASTA sequence analysis
• Mutation system implementation
• ESM model embeddings integration
• FastAPI service development
• Unit tests and documentation
• Deployment and CI/CD

📚 Learning Goals

• Master protein sequence analysis and manipulation
• Understand transformer-based protein language models
• Build production-ready BioAI applications
• Contribute to open-source computational biology tools

🤝 Contributing

This is a personal learning project, but suggestions and feedback are welcome!

📝 License

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

🔗 Links

• GitHub Repository
• EvolutionaryScale - Target company inspiration

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