A visualisation tool for protein embeddings from pLMs
Project description
ProtSpace
ProtSpace is a visualization tool for exploring protein embeddings or similarity matrices. It projects high-dimensional protein language model data into 2D space, color-codes proteins by biological annotations, and exports publication-ready figures.
- Multiple projections: PCA, UMAP, t-SNE, MDS, PaCMAP
- Automatic annotations: UniProt, InterPro, and Taxonomy
- Structure viewer: Integrated protein structure visualization
- Export: PNG, PDF, SVG, HTML
🌐 Try Online
ProtSpace Web (recommended): Fast 2D explorer optimized for large datasets — drag & drop .parquetbundle files (source)
Legacy Dash frontend: Original interface with 3D support (slow with large datasets)
🚀 Google Colab Notebooks
Note: Use Chrome or Firefox for best experience.
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Generate Protein Embeddings:
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Prepare ProtSpace Bundle:
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Full Pipeline Demo:
📦 Installation
pip install protspace
🎯 Quick Start
1. Process local data
protspace-local -i embeddings.h5 -o output_dir -m pca2,umap2
2. Explore results
Upload the generated .parquetbundle file at protspace.app/explore.
📊 Example Output
✨ Annotations
Use -a to color-code proteins by UniProt, InterPro, or Taxonomy annotations. Groups (default, all, uniprot, interpro, taxonomy) and individual names can be mixed freely. If -a is omitted, the default group is used.
protspace-local -i data.h5 # default UniProt annotations (fast)
protspace-local -i data.h5 -a default,interpro,kingdom # mix groups and individual names
📖 Documentation
- Annotation Reference — full list of annotations, groups, data sources, output formats
- Annotation Styling — custom colors, shapes, sort modes, and the
--generate-templateworkflow - CLI Reference — command options, method parameters, file formats
📝 Citation
Senoner T, Olenyi T, Heinzinger M, Spannagl A, Bouras G, Rost B, Koludarov I. ProtSpace: A Tool for Visualizing Protein Space. Journal of Molecular Biology, 168940, 2025. doi:10.1016/j.jmb.2025.168940
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