BioChain Docking Agent

Overview

BioChain Docking Agent is an advanced, AI-powered decentralized application (dApp) designed to streamline the analysis and verification of molecular docking simulations. It bridges the gap between computational chemistry and blockchain technology by providing a platform where researchers can upload docking results, receive instant AI-generated insights via a Live Agent, visualize molecular structures, and immutably verify their findings on the Solana blockchain.

This platform addresses the need for transparency, reproducibility, and rapid analysis in the drug discovery pipeline.

Key Features

1. Job Management: A centralized dashboard to track status, scores, and metadata of multiple docking experiments.
2. AI-Driven Analysis (Gemini 3):
   • Executive Summaries: Utilizes gemini-3-pro-preview with "Thinking" capabilities to generate deep technical summaries of docking scores and binding efficiencies.
   • Live Agent Chat: An interactive chat interface powered by gemini-3-flash-preview allows researchers to ask specific questions about the molecule's properties in real-time.
3. Advanced Visualization: Interactive 3D molecular structure viewer with rotation, pan/zoom controls, hydrogen bond toggles, and snapshot export capabilities.
4. On-Chain Verification (Solana Devnet): "Sign" scientific results on the Solana blockchain, creating a permanent, tamper-proof record (Proof of Computation) for intellectual property and audit trails.
5. Professional Reporting: Generates comprehensive PDF reports that include high-resolution snapshots of visualizations, charts, and the AI-generated analysis.

Solana Service & Architecture (Devnet)

BioChain uses the Solana Blockchain (Devnet) as an immutable public ledger to verify scientific data.

How it Works

Instead of deploying a custom smart contract (Program) for every data entry, BioChain utilizes the Memo Program to attach structured binary data to transaction logs. This ensures extremely low costs and high throughput while maintaining cryptographic proof of existence.

• Network: Solana Devnet (https://api.devnet.solana.com)
• Program ID: MemoSq4gqABAXKb96qnH8TysNcWxMyWCqXgDLGmfcQb (SPL Memo Program)
• Data Serialization: Borsh (Binary Object Representation Serializer for Hashing).
  • Data is packed into a compact binary format before being sent to the chain.
  • The frontend deserializes this binary data directly from the blockchain node to verify integrity.

Data Schema

The following structure is serialized and stored on-chain:

struct DockingReport {
    jobId: String,        // Unique Job Identifier
    moleculeName: String, // Name of the compound
    score: f64,          // Docking Score (kcal/mol)
    timestamp: u64        // Unix Timestamp of verification
}

Wallet Requirements

To interact with the verification features, you must:

1. Install the Phantom Wallet browser extension.
2. Switch your wallet network to Devnet.
3. Obtain free Devnet SOL (Solana Faucet) to pay for transaction gas fees (usually < 0.00001 SOL).

Technology Stack

Frontend

• React 19: Leveraging concurrent rendering.
• TypeScript: Strict type safety for scientific data.
• Tailwind CSS: Scientific/Dark mode aesthetic.
• Vite: Build tooling.

AI & Data

• Google GenAI SDK:
  • gemini-3-pro-preview: Complex reasoning for reports.
  • gemini-3-flash-preview: Low latency for interactive chat.
• Recharts: SVG-based data visualization.
• jsPDF / html2canvas: Report generation.

Blockchain

• @solana/web3.js: Interaction with Solana nodes.
• Borsh: Binary serialization for on-chain data storage.

Getting Started

1. Clone the repository
2. Install dependencies:

   npm install

3. Configure Environment: Create a .env file in the root directory and add your Google Gemini API Key:

   API_KEY=your_google_api_key_here

4. Run Development Server:

   npm run dev

5. Open in Browser: Navigate to http://localhost:5173.

Usage Guide

1. Upload: Drag and drop a .pdbqt, .sdf, or .out file. The system will auto-parse metrics like Docking Score and Molecular Weight.
2. Analyze: View the generated charts and 3D visualization. Wait for the Gemini Agent to generate the textual summary.
3. Chat: Switch to the "Ask AI" tab to discuss specific binding modes or optimization strategies with the agent.
4. Connect Wallet: Click "Connect Phantom" (ensure you are on Devnet).
5. Verify: Click "Verify" to sign a transaction. Once confirmed, a green checkmark and Transaction Hash will appear.
6. Audit: Go to the "Audit" tab to fetch the data live from the Solana blockchain and compare it against the local app data to ensure integrity.
7. Export: Click "Export PDF" to download the full report.