ProtPeek
A lightweight desktop widget for rapid visualization of 3D protein structures from PDB and AlphaFold databases.
Scientific Overview
ProtPeek enables researchers, educators, and students to quickly visualize three-dimensional protein structures in real-time. Whether you're studying known crystallographic structures from the RCSB Protein Data Bank (PDB) or exploring AI-predicted structures from AlphaFold, ProtPeek provides an intuitive interface for interactive molecular visualization.
Key Capabilities
The widget supports:
- PDB Code Input: Direct lookup of crystallographic structures (e.g., 1UBQ for ubiquitin)
- UniProt ID Input: Access to AlphaFold predicted structures (e.g., Q92793)
- Multiple Visualization Styles: Cartoon ribbon and ball-and-stick representations
- Real-time Rotation: Automated clockwise rotation for structure examination
- Lightweight Design: 200×200 pixel always-on-top widget for non-intrusive desktop integration
Features
Dual Data Sources
Access both experimental (RCSB PDB) and predicted (AlphaFold) protein structures
Multiple Representations
Switch between cartoon ribbon and ball-and-stick visualization styles
Lightweight & Fast
Minimal footprint with instant structure loading and rotation
Always-On-Top
Desktop widget that stays visible while you work in other applications
WebGL Visualization
Powered by 3Dmol.js for interactive, hardware-accelerated rendering
Real-time Rotation
Automated clockwise rotation for comprehensive structure examination
Get Started
Download ProtPeek for Windows (64-bit)
Single executable file • No installation required • Self-contained
📥 Download ProtPeek.exe (v1.0)Note: The 3Dmol.js library is bundled with the executable.
Quick Start Guide
Using ProtPeek
- Launch the ProtPeek executable
- Enter a PDB code (4 characters, e.g.,
1UBQ) or UniProt ID (6+ characters, e.g.,Q92793) - Select visualization style (Cartoon or Ball & Stick)
- Click Play to load and visualize the structure
- Watch as the structure rotates for full 3D examination
Example Structures
PDB Examples:
• 1UBQ - Ubiquitin (small regulatory protein)
• 2HHB - Hemoglobin (oxygen transport)
• 1MBN - Myoglobin (oxygen storage)
UniProt Examples:
• Q92793 - AlphaFold predicted structure
• P12345 - Another example UniProt ID
🤝 Help Us Expand
We're seeking community contributions to build and maintain ProtPeek binaries for additional operating systems.
Current Platform Support
If you can build and test ProtPeek for other platforms, we'd love your contribution! Please submit binaries via pull request to our GitHub repository.
🔗 Contribute on GitHubTechnical Information
Technology Stack
Frontend: 3Dmol.js (WebGL-based molecular visualization)
Backend: Python 3.8+ with PyQt5 and PyQtWebEngine
Data Sources:
- RCSB Protein Data Bank (PDB) - Experimental structures
- UniProt/AlphaFold - AI-predicted structures
Scientific Foundations
Molecular Visualization: This application utilizes 3Dmol.js, a powerful JavaScript library for real-time molecular visualization with WebGL acceleration.
Rego, N., & Koes, D. (2015). 3Dmol.js: molecular visualization with WebGL. Bioinformatics, 31(8), 1322–1324.
https://doi.org/10.1093/bioinformatics/btu829
Data Quality: The RCSB PDB contains experimentally determined protein structures solved using X-ray crystallography, NMR spectroscopy, cryo-EM, and other methods. AlphaFold structures represent high-confidence AI predictions for proteins without experimental structures.