MoleCuQuest

Advanced Molecular Research Platform

Exploring the Molecular Frontier - Innovation in Chemical Research

1. Introduction
2. Features
3. Platform Overview
4. Technology Stack
5. Installation
6. Environment Configuration
7. Usage Guide
8. API Integration
9. Project Structure
10. Contributing
11. LICENSE

MoleCuQuest is a cutting-edge molecular research platform that combines AI-driven molecule generation with comprehensive chemical analysis capabilities. Built with modern web technologies and powered by NVIDIA's advanced machine learning models, MoleCuQuest enables researchers to accelerate drug discovery and molecular design processes.

The platform integrates state-of-the-art algorithms for protein structure prediction, molecular docking simulations, and real-time molecular visualization, making it an essential tool for pharmaceutical researchers, chemists, and bioinformatics professionals.

• AI-Powered Molecule Generation: Utilizes NVIDIA MolMIM for generating novel molecular structures with desired properties
• Real-time 3D Molecular Visualization: Interactive molecular structure rendering using RDKit
• Comprehensive Chemical Analysis: Integration with PubChem for extensive compound research
• Collaborative Research Environment: Real-time team collaboration with messaging and project sharing
• Molecular Property Analysis: Advanced algorithms for molecular property optimization
• Drug Discovery Support: Tools and metrics for pharmaceutical research applications

• CMA-ES Algorithm: Covariance Matrix Adaptation Evolution Strategy for molecular optimization
• QED Scoring: Quantitative Estimate of Drug-likeness for pharmaceutical applications
• SMILES Integration: Support for both Canonical and Isomeric SMILES representations
• User Authentication: Secure user management with NextAuth.js
• Responsive Design: Optimized for desktop, tablet, and mobile devices

The central hub providing access to all platform features with an intuitive interface for navigation and project management.

Advanced molecular generation interface powered by NVIDIA MolMIM, allowing researchers to create novel compounds with specific properties.

Real-time molecular structure visualization with support for complex molecular architectures and ring structures.

Advanced chemical representation supporting wedge-dash notation for stereochemical information.

Comprehensive database of molecular structures with advanced search and filtering capabilities.

Real-time messaging and collaboration tools for research teams.

• Next.js 14: React framework with App Router for modern web applications
• TypeScript: Type-safe development for enhanced code quality
• Tailwind CSS: Utility-first CSS framework for responsive design
• Lucide React: Modern icon library for consistent UI elements

• NVIDIA NIM: Advanced AI models for molecular generation and analysis
• MongoDB Atlas: Cloud-based NoSQL database for scalable data storage
• NextAuth.js: Comprehensive authentication solution
• PubChem API: Chemical database integration for compound research

• RDKit: Open-source cheminformatics toolkit for molecular manipulation
• SMILES: Simplified molecular-input line-entry system
• CMA-ES: Evolutionary algorithm for molecular optimization

• Ably: Real-time messaging and collaboration features
• Resend: Email service for user notifications

Ensure you have the following installed:

• Node.js (v18 or higher)
• npm or yarn package manager
• Git for version control

git clone https://github.com/HarshTomar1234/MoleCuQuest.git
cd MoleCuQuest

npm install
# or
yarn install

Create a .env file in the project root with the following configuration:

# NVIDIA API Configuration
NEXT_PUBLIC_NVIDIA_API_KEY=your-nvidia-api-key

# Database Configuration
MONGODB_URL=your-mongodb-atlas-connection-string

# Authentication
NEXTAUTH_SECRET=your-secure-random-string
NEXTAUTH_URL=http://localhost:3000

# Application Settings
NEXT_PUBLIC_API_BASE_URL=http://localhost:3000

# Optional Services
ABLY_API_KEY=your-ably-api-key
RESEND_KEY=your-resend-api-key

1. Visit NVIDIA Build Platform
2. Create a free developer account
3. Generate your API key for MolMIM access

1. Create account at MongoDB Atlas
2. Set up a free cluster
3. Configure database access and network settings
4. Obtain connection string

npm run dev

Access the application at http://localhost:3000

npm run build
npm start

1. Navigate to the "Generate Molecule" section
2. Input base molecular structure (SMILES format)
3. Configure generation parameters:
   • Number of molecules to generate
   • Similarity threshold
   • Optimization particles and iterations
4. Execute generation using NVIDIA MolMIM
5. Review and analyze generated molecular structures

1. Access the "Search Compounds" feature
2. Enter compound name or identifier
3. View comprehensive molecular data including:
   • Molecular formula and weight
   • Chemical identifiers (InChI, SMILES)
   • Physical and chemical properties
   • 3D molecular visualization

1. Create or join research teams
2. Share molecular data and research findings
3. Real-time messaging and project discussions
4. Collaborative molecule analysis and review

The platform integrates with NVIDIA's MolMIM for advanced molecular generation:

const response = await fetch(invokeUrl, {
  method: "POST",
  headers: {
    Authorization: `Bearer ${API_KEY}`,
    Accept: "application/json",
    "Content-Type": "application/json",
  },
  body: JSON.stringify({
    algorithm: "CMA-ES",
    num_molecules: 10,
    property_name: "QED",
    minimize: false,
    min_similarity: 0.3,
    particles: 30,
    iterations: 10,
    smi: inputSMILES,
  }),
});

For comprehensive compound data retrieval:

const pubchemUrl = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${compoundName}/property/MolecularFormula,MolecularWeight,InChIKey,CanonicalSMILES,IsomericSMILES,IUPACName,XLogP,ExactMass,MonoisotopicMass,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,HeavyAtomCount/JSON`;

MoleCuQuest/
├── public/
│   ├── platform_images/     # Platform screenshots and demos
│   └── images/              # Static assets and icons
├── src/
│   ├── app/                 # Next.js App Router pages
│   │   ├── api/            # API routes and server actions
│   │   ├── auth-page/      # Authentication pages
│   │   ├── model/          # Molecule generation interface
│   │   ├── research/       # Compound research tools
│   │   └── message/        # Collaboration features
│   ├── components/         # Reusable UI components
│   │   ├── MoleculeStructure/  # Molecular visualization
│   │   ├── dashboard/      # Dashboard components
│   │   └── Layouts/        # Page layouts
│   ├── lib/               # Utility functions and configurations
│   │   ├── actions/       # Server actions
│   │   ├── database/      # Database models and connections
│   │   └── utils.ts       # Helper functions
│   └── types/             # TypeScript type definitions
├── next.config.js         # Next.js configuration
├── tailwind.config.ts     # Tailwind CSS configuration
└── package.json          # Project dependencies

We welcome contributions to MoleCuQuest! To contribute:

1. Fork the repository
2. Create a feature branch: git checkout -b feature/amazing-feature
3. Commit your changes: git commit -m 'Add amazing feature'
4. Push to the branch: git push origin feature/amazing-feature
5. Open a Pull Request

• Follow TypeScript best practices
• Ensure responsive design compatibility
• Write clear, documented code
• Test molecular generation features thoroughly
• Maintain API integration standards

• Use TypeScript for all new code
• Follow ESLint and Prettier configurations
• Implement proper error handling
• Write comprehensive component documentation

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