Protein Function Prediction - CAFA 6 Challenge

A full-stack web application for protein function prediction using ESM-2 and AlphaFold 2 ensemble models.

🚀 Quick Start

Prerequisites

• Node.js (v16 or higher)
• npm or yarn

Installation

1. Clone the repository

git clone <your-repo-url>
cd protein-prediction-app

2. Install Backend Dependencies

cd server
npm install

3. Install Frontend Dependencies

cd ../client
npm install

Running the Application

1. Start the Backend Server (Terminal 1)

cd server
npm run dev

Backend will run on http://localhost:5000 2. Start the Frontend (Terminal 2)

cd client
npm run dev

Frontend will run on http://localhost:5173 3. Open your browser and navigate to http://localhost:5173

📁 Project Structure

protein-prediction-app/
├── server/              # Backend (Node.js + Express)
│   ├── server.js       # Main server file
│   ├── routes/         # API routes
│   └── package.json    # Backend dependencies
├── client/              # Frontend (React + Vite)
│   ├── src/
│   │   ├── components/ # React components
│   │   ├── pages/      # Page components
│   │   ├── App.jsx     # Main app component
│   │   └── main.jsx    # Entry point
│   └── package.json    # Frontend dependencies
└── README.md

🔌 API Endpoints

POST /api/predict

Accepts protein sequence and returns GO term predictions. Request:

{
  "sequence": "MKTAYIAKQRQISFVK..."
}

Response:

[
  {
    "GO_term": "GO:0009274",
    "name": "Peptidoglycan-based cell wall",
    "probability": 0.931,
    "ontology": "CC"
  }
]

GET /api/project-info

Returns project metadata and objectives.

🧬 Features

• Interactive Demo: Upload FASTA files or paste sequences
• Mock Predictions: Simulated GO term predictions
• Responsive Design: Works on all devices
• Modern UI: Built with Tailwind CSS and React

🛠️ Technologies

• Frontend: React, Vite, Tailwind CSS
• Backend: Node.js, Express, CORS
• Styling: Tailwind CSS

📝 Notes

• Current version uses mock predictions
• To integrate real models (ESM-2, AlphaFold 2), update /api/predict endpoint in server/routes/api.js

👥 Team

Research project for CAFA 6 Challenge - Critical Assessment of Functional Annotation

📄 License

MIT License