💊 Protein 3D Modeler & Drug Discovery

An interactive, high-performance web application designed for structural biologists, bioinformaticians, and computational chemists. This tool allows users to visualize complex 3D protein structures, extract precise metadata, and perform preliminary ligand binding site analysis directly in the browser.

Built with Streamlit and py3Dmol, and natively integrated with the RCSB Protein Data Bank (PDB) API.

🚀 Live Demo: https://protein-3d-modeler.streamlit.app

---

🎯 Who is this for?

• Bioinformaticians & Computational Chemists: For rapid visual inspection of protein-ligand complexes before running heavy docking simulations (like AutoDock Vina).
• Structural Biologists: To analyze secondary structures, B-factors, and macromolecular assemblies without opening heavy desktop software like PyMOL or Chimera.
• Students & Researchers: An accessible, zero-install educational tool to explore molecular biology in full 3D.

🧬 Key Features

• Real-time 3D Rendering Engine: Renders massive macromolecular complexes instantly using Py3Dmol.
• Direct RCSB Database Integration: Instantly fetches the structure alongside exact metadata (Organism, Title, Experimental Method).
• Customizable Visualization Styles:
  • Ribbon (Cartoon): Best for viewing overall protein folding, alpha-helices, and beta-sheets.
  • Stick: Ideal for analyzing individual atomic bonds, side-chain conformations, and ligand interactions.
  • Sphere (Space-filling): Visualizes the Van der Waals radii of atoms, useful for seeing the overall volume and shape.
  • Surface: Generates the solvent-accessible surface area (SASA), crucial for identifying binding pockets and surface electrostatics.
• Dynamic Color Schemes:
  • Spectrum: Colors the chain from N-terminus to C-terminus (rainbow).
  • Chain: Differentiates multiple protein chains in a complex.
  • Secondary Structure: Highlights helices and sheets.
  • B-factor: Visualizes thermal mobility (flexibility) of different regions.
• AI Target Analysis (Mockup): A demonstration of highlighting potential small-molecule inhibitor binding pockets.
• Export & Download: Download the raw .pdb file directly from the interface for offline use.

📸 Screenshots & Visual Styles

Here you can see the engine in action across different modes:

1. Ribbon (Cartoon) Style & Secondary Structure

Perfect for viewing the overall backbone architecture and folding patterns.

2. Stick Style & Spectrum Coloring

Atomic-level resolution for a deep dive into side-chains and interactions.

3. Sphere Rendering (Space-filling)

Visualizing the Van der Waals radii of atoms to see overall molecular volume.

4. Surface Topology & Binding Pockets

Visualizing the exterior topology of the macromolecule to find active sites.

5. PDB Metadata Extraction & UI

Real-time structural info fetching directly from the RCSB Database.

6. AI Target Analysis & Drug Binding Pockets

Highlighting and isolating potential active sites (pockets) for small-molecule inhibitor binding on specific chains.

🚀 Installation & Usage

1. Clone the repository:

   git clone https://github.com/your-username/protein-3d-modeler.git
   cd protein-3d-modeler

2. Install dependencies:

   pip install streamlit py3Dmol stmol requests

3. Run the application:

   streamlit run app.py

🛠️ Tech Stack

• Frontend/Backend: Streamlit
• 3D Engine: py3Dmol & stmol
• Biological Data API: RCSB PDB REST API

---

Contact

Juliia Nuzhnenko

• Email: julia.n@forneus.io
• LinkedIn: Juliia Nuzhnenko

Powered by Forneus Technologies