What is ProtSpace?
ProtSpace is a browser-based, interactive visualization tool for exploring protein language model (pLM) embeddings. It helps researchers and biologists understand high-dimensional protein data by visualizing it in 2D.
Why Use ProtSpace?
Protein language models (like ProtT5, ESM2, Ankh) create embeddings that capture biological information in hundreds or thousands of dimensions. ProtSpace helps you:
- See patterns: Visualize how proteins cluster based on their embeddings
- Explore relationships: Find proteins with similar properties
- Discover insights: Identify functional groupings and evolutionary clusters
- Share findings: Export figures or the dataset itself for others to explore
Key Features
| Feature | Description |
|---|---|
| No Installation | Runs entirely in your browser at protspace.app |
| Privacy-First | Your data never leaves your computer - all processing is client-side |
| Multiple Views | PCA, UMAP, t-SNE, MDS, and PaCMAP projections |
| Rich Annotations | Color by taxonomy, function, family, or any annotation |
| 3D Structures | View protein structures from AlphaFold via 3D-Beacons API |
| Export Options | Save images (PNG, PDF), data (JSON), and protein IDs |
How It Works
- Prepare data: Generate a
.parquetbundlefile using our Google Colab notebook or Python CLI - Load file: Drag & drop onto the Explore page
- Explore: Navigate, filter, and discover patterns in your protein data
Privacy and Security
ProtSpace processes everything locally in your browser:
- No uploads: Files never leave your computer
- No tracking: We don't collect any usage data
- Open source: Fully transparent codebase on GitHub
Use Cases
- Functional Analysis: Group proteins by predicted function
- Evolutionary Studies: Identify convergent evolution patterns
- Quality Control: Check embedding model outputs for biases
- Education: Teach protein bioinformatics interactively
- Publication: Create figures for papers and presentations
Performance
ProtSpace can handle datasets with 200,000+ proteins directly in your browser without server uploads.
Next Steps
- Quick Start - Get started in 5 minutes
- Using Google Colab - Prepare your data
- Using the Explore Page - Learn all the features