Protviz: Protein Annotation Visualizer

Language Python Support License Python Tests

ProtViz is a Python package designed to simplify the retrieval and visualization of protein annotations and structural information. It provides a powerful and intuitive way to fetch data from multiple bioinformatics databases and plot this information along a protein sequence using a flexible track-based system.

Key Features

Protviz simplifies complex protein data visualization with a range of powerful features:

  • Comprehensive Data Retrieval:
    • Fetch protein sequence length directly from UniProt.
    • Retrieve PDB structure coverage and detailed ligand interaction data from the Protein Data Bank in Europe (PDBe).
    • Get domain annotations from the TED database.
    • Fetch per-residue confidence scores (pLDDT) and AlphaMissense pathogenicity predictions from the AlphaFold Database (AFDB).
    • Access domain information from InterPro member databases like Pfam and CATH-Gene3D.

  • Flexible Track-Based Visualization: Protviz employs an intuitive track system to display diverse annotations:
    • AxisTrack: Essential for displaying the sequence axis and length context.
    • PDBTrack: Clearly shows regions covered by PDB structures, with options for detailed or collapsed views.
    • LigandInteractionTrack: Highlights residues involved in ligand binding.
    • TEDDomainsTrack: Visualizes domains as defined by the TED database.
    • AlphaFoldTrack: Displays AlphaFold’s pLDDT and AlphaMissense scores along the sequence.
    • InterProTrack: Shows domain signatures from various InterPro member databases.
    • CustomTrack: Offers the ultimate flexibility to plot your own arbitrary annotations, whether they are sequence ranges or specific point features, with full control over appearance.

  • User-Friendly Plotting:
    • Seamlessly combine multiple tracks into a single, coherent, and easy-to-interpret figure.
    • Effortlessly zoom into specific regions of the protein sequence for detailed analysis.
    • Conveniently save your plots in high quality for presentations and publications.

Get Started Quickly

Jump right in by following our Getting Started guide, or explore the Core Components to understand the data retrieval clients and visualization tracks in detail.

Dependencies

Protviz relies on a few key Python libraries:

  • numpy>=1.20
  • matplotlib>=3.4
  • requests>=2.20
  • gemmi (specifically for parsing CIF files when fetching data from the AlphaFold Database)

We recommend installing Protviz in a dedicated virtual environment.

License

ProtViz is distributed by an MIT license