Molecular Docking Platform

A professional full-stack web application for molecular docking using AutoDock Vina. This application provides an intuitive interface for submitting docking jobs, monitoring progress, and analyzing results.

🚀 Features

• Modern React Frontend: Built with TypeScript, Material-UI, and professional UX design
• FastAPI Backend: High-performance Python backend with async support
• AutoDock Vina Integration: Professional molecular docking with configurable parameters
• Real-time Job Monitoring: Live status updates and progress tracking
• Interactive Results: Sortable tables, best result highlighting, and downloadable outputs
• Professional Architecture: Clean separation of concerns with proper project structure

🏗️ Project Structure

windsurf-project/
├── backend/
│   ├── src/
│   │   ├── core/
│   │   │   ├── config.py          # Application configuration
│   │   │   └── __init__.py
│   │   ├── models/
│   │   │   ├── schemas.py         # Pydantic models
│   │   │   └── __init__.py
│   │   ├── routers/
│   │   │   ├── docking.py         # Docking endpoints
│   │   │   ├── health.py          # Health check
│   │   │   └── __init__.py
│   │   ├── services/
│   │   │   ├── vina_service.py    # AutoDock Vina integration
│   │   │   └── __init__.py
│   │   ├── main.py                # FastAPI application
│   │   └── __init__.py
│   └── requirements.txt
├── frontend/
│   ├── public/
│   │   ├── index.html
│   │   └── manifest.json
│   ├── src/
│   │   ├── components/
│   │   │   ├── DockingUpload.tsx  # File upload and parameter configuration
│   │   │   ├── JobStatus.tsx      # Real-time job monitoring
│   │   │   └── Results.tsx        # Results visualization
│   │   ├── services/
│   │   │   └── api.ts             # API client
│   │   ├── types/
│   │   │   └── index.ts           # TypeScript type definitions
│   │   ├── App.tsx                # Main application component
│   │   └── index.tsx              # Application entry point
│   ├── package.json
│   └── tsconfig.json
└── README.md

🛠️ Installation

Prerequisites

• Node.js (v16 or higher)
• Python 3.8+
• AutoDock Vina
• AutoDockTools (prepare_receptor4.py, prepare_ligand4.py)

Backend Setup

1. Navigate to the backend directory:

cd backend

2. Create a virtual environment:

python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

3. Install dependencies:

pip install -r requirements.txt

4. Create a .env file (optional):

ALLOWED_ORIGINS=["http://localhost:3000"]
VINA_EXECUTABLE=vina
MAX_FILE_SIZE=104857600

5. Start the backend server:

cd src
python main.py

The API will be available at http://localhost:8000 with documentation at http://localhost:8000/api/docs.

Frontend Setup

1. Navigate to the frontend directory:

cd frontend

2. Install dependencies:

npm install

3. Start the development server:

npm start

The frontend will be available at http://localhost:3000.

🔬 Usage

1. Submit Docking Job

• Upload a receptor file (PDB/PDBQT format)
• Upload one or more ligand files (PDB/PDBQT/SDF/MOL2 formats)
• Configure docking parameters:
  • Binding site center coordinates (X, Y, Z)
  • Search space dimensions
  • Exhaustiveness and number of modes
• Submit the job and receive a unique job ID

2. Monitor Progress

• Track job status in real-time
• View progress indicators and statistics
• Get detailed information about successful and failed docks

3. Analyze Results

• View sortable results table with binding affinities and RMSD values
• Identify the best docking result with highlighted metrics
• Download result files for further analysis
• Quality assessment with color-coded indicators

🧪 API Endpoints

Health Check

• GET /api/health - Service health status

Docking Operations

• POST /api/docking/submit - Submit new docking job
• GET /api/docking/status/{job_id} - Get job status and results
• GET /api/docking/results/{job_id} - Download result files
• DELETE /api/docking/job/{job_id} - Delete job and cleanup files

🎨 UI Features

• Material Design: Modern, professional interface using Material-UI
• Responsive Layout: Works seamlessly on desktop and mobile devices
• Drag & Drop: Intuitive file upload with drag-and-drop support
• Real-time Updates: Live job status monitoring with automatic refresh
• Data Visualization: Interactive tables with sorting and filtering
• Progress Indicators: Visual feedback for long-running operations

🔧 Configuration

Docking Parameters

• Binding Site Center: X, Y, Z coordinates of the binding site
• Search Space Size: Dimensions of the search area in Angstroms
• Exhaustiveness: Search thoroughness (1-32, default: 8)
• Number of Modes: Binding poses to generate (1-20, default: 9)

File Formats

Supported Receptor Formats:

• PDB (Protein Data Bank)
• PDBQT (AutoDock format)

Supported Ligand Formats:

• PDB (Protein Data Bank)
• PDBQT (AutoDock format)
• SDF (Structure Data File)
• MOL2 (Tripos format)

🚦 Development

Backend Development

The backend uses FastAPI with a clean architecture:

• Models: Pydantic schemas for request/response validation
• Services: Business logic and AutoDock Vina integration
• Routers: API endpoints and HTTP handling
• Core: Configuration and shared utilities

Frontend Development

The frontend is built with React and TypeScript:

• Components: Reusable UI components with Material-UI
• Services: API client with error handling
• Types: TypeScript definitions for type safety
• State Management: React hooks for local state

📝 License

This project is licensed under the MIT License.

🤝 Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Add tests if applicable
5. Submit a pull request

📞 Support

For questions or issues, please open a GitHub issue or contact the development team.

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Built with ❤️ using React, FastAPI, and AutoDock Vina