RNAbridge 🧬

RNAbridge is a professional platform for the analysis of RNA structural motifs. It automates the extraction, categorization, and visualization of complex super-helices and junctions from CIF data, providing a searchable database with interactive 2D and 3D perspectives.

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🖼️ Visual Overview

Integrated Structural Preview	Statistical Insights
Synchronized 2D & 3D Viewer	Automated Geometry Statistics

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✨ Key Features

• Automated Pipeline: Single-pass analysis from raw CIF files to a structured database.
• Advanced Geometry: Detailed calculation of bend angles, stacking interactions, and coaxial pairings.
• Rich Visuals: Automatic generation of SVG diagrams (via VARNA) and PyMOL scripts.
• Modern Interface: React-based dashboard with Mol* integration for seamless 3D viewing.
• Flexible Storage: Native support for PostgreSQL (production) and SQLite (portable).

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🚀 Quick Start (Docker - Recommended)

The easiest way to run the full stack (Backend, Frontend, and Database) with all system dependencies pre-configured.

1. Prepare X3DNA

Due to licensing, you must provide your own X3DNA distribution:

1. Download X3DNA v2.4 from x3dna.org.
2. Extract it into the x3dna-v2.4/ directory in the project root.

2. Launch

docker-compose up --build

• Web Interface: http://localhost:8000
• API Documentation: http://localhost:8000/docs

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🛠️ Installation & Local Development

If you prefer to run RNAbridge locally (e.g., for development), ensure the following prerequisites are met:

Prerequisites

Tool	Purpose	Note
Python 3.12+	Main Logic	Required
Docker	Visualizations	Required for cli2rest-bio (VARNA)
X3DNA (v2.4)	Helix Analysis	Must be in x3dna-v2.4/
Node.js	Frontend	Only for npm run dev
PyMOL	3D Processing	Recommended

Setup Options

Option A: Conda (Recommended for Dev)

conda env create -f environment.yml
conda activate rnabridge
# Build frontend once
cd frontend && npm install && npm run build && cd ..
# Start server
python api.py

Option B: Pip

pip install -r requirements.txt
python api.py

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📖 Usage Guide

1. Run Analysis Pipeline

Place your .cif files in the cif/ directory, then trigger the processing:

Using Docker:

docker-compose exec app bash pipeline.sh

Using Local Python:

./pipeline.sh

2. Accessing the Interface

• Web Interface: http://localhost:8000

• API Documentation:

  • Swagger UI: http://localhost:8000/docs
  • ReDoc: http://localhost:8000/redoc

• Development Mode (Local):

  • Backend: python api.py (serves API at :8000)
  • Frontend (Live Reload): cd frontend && npm run dev (available at :5173)

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⚙️ Configuration

RNAbridge uses a centralized config.py. Key environment variables:

• DATABASE_URL: Connection string. Defaults to SQLite (sqlite:///rnabridge.db).
  • PostgreSQL Example: export DATABASE_URL="postgresql://user:password@localhost:5432/rnabridge"
• X3DNA: Path to X3DNA installation (default: ./x3dna-v2.4).

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📄 Data Sources & Licensing

• Project License: This project is licensed under the MIT License.
• X3DNA: Users must obtain their own license from x3dna.org.
• RCSB PDB: Structural data is fetched from the Protein Data Bank.

👥 Authors

• Damian Zakrzewski
• Tomasz Zok
• Maciej Antczak