ProtSpace Web

ProtSpace Web is a browser-based visualization tool for exploring protein language model (pLM) embeddings. Built with modular web components (canvas renderer, interactive legend, control bar), it enables interactive exploration through dimensionality reduction methods (PCA, UMAP, t-SNE) with zoom, pan, and selection. Color by features, view 3D protein structures, and export images or data files for sharing.

🌐 Try Online

Demo: https://protspace.app/ → Drag & drop .parquetbundle files

🚀 Prepare Your Data

Option 1: Google Colab (no local installation needed)

Generate .parquetbundle files directly in your browser:

Option 2: Python ProtSpace (local installation)

pip install protspace

# Query UniProt and generate visualization files
protspace-query -q "(ft_domain:phosphatase) AND (reviewed:true)" -o output_dir

# Or use your own embeddings
protspace-local -i embeddings.h5 -o output_dir

See the Python ProtSpace repository for details.

📚 Documentation

Full Documentation - User guides, data preparation, and feature explanations.

🔧 Development

git clone https://github.com/tsenoner/protspace_web.git
cd protspace_web
pnpm install
pnpm dev  # App: http://localhost:8080 | Docs: http://localhost:5174/docs/

🧹 Code Quality

Before committing, run:

pnpm precommit

This runs formatting (Prettier), linting (ESLint), and type checking in one command.

⚖️ License

Apache License 2.0 - see LICENSE