Protviz: Protein Annotation Visualiser

Protviz is a Python package designed to retrieve and visualize various protein annotations and structural information. It allows users to fetch data from multiple bioinformatics databases and plot this information along a protein sequence using a flexible track-based system.

Features

• Data Retrieval:
  • Fetch protein sequence length from UniProt.
  • Retrieve PDB coverage and ligand interaction data from PDBe.
  • Get TED domain annotations from the TED database.
  • Fetch pLDDT scores and AlphaMissense data from the AlphaFold Database (AFDB).
• Track-Based Visualization:
  • AxisTrack: Displays the sequence axis with tick marks.
  • PDBTrack: Shows PDB structure coverage, with options to display as individual entries or a collapsed overview.
  • LigandInteractionTrack: Visualizes ligand binding sites on the protein.
  • TEDDomainsTrack: Displays TED domain annotations.
  • AlphaFoldTrack: Shows AlphaFold prediction metrics like pLDDT and average AlphaMissense pathogenicity scores.
  • CustomTrack: Allows plotting of arbitrary user-defined annotations (ranges or points) with customizable labels and colors.
• Core Plotting Functionality:
  • Combines multiple tracks into a single, coherent plot.
  • Supports zooming into specific regions of the protein sequence.
  • Option to save plots to a file.