Features of Protviz

Protviz is equipped with a comprehensive suite of features designed to streamline the process of fetching, integrating, and visualising diverse protein annotations. Below is a more detailed look at what Protviz offers:

1. Extensive Data Retrieval Capabilities

Protviz connects to major bioinformatics databases, allowing you to gather a wide array of protein information with ease:

  • UniProt Integration:
    • Quickly fetch the authoritative sequence length for any protein using its UniProt ID, forming the basis for all sequence-scaled visualisations.
  • PDBe (Protein Data Bank in Europe) Connectivity:
    • Structural Coverage: Identify which regions of a protein have been experimentally determined and are available in PDB structures.
    • Ligand Interactions: Pinpoint specific residues involved in binding to various ligands, crucial for understanding protein function and drug design.
  • TED Database Access:
    • Retrieve domain annotations from the TED (The Encyclopedia of Domains) database, often including CATH superfamily classifications.
  • AlphaFold Database (AFDB) Integration:
    • pLDDT Scores: Fetch and visualise per-residue confidence scores (pLDDT) from AlphaFold predictions, offering insights into model quality.
    • AlphaMissense Data: Access AlphaMissense pathogenicity predictions to evaluate the potential impact of missense variants.
  • InterPro Database Support:
    • Gain access to a wealth of domain and feature annotations from various InterPro member databases, such as:
      • Pfam: Visualise curated protein families and domains.
      • CATH-Gene3D: Display structural domain classifications.

2. Versatile Track-Based Visualisation

Protviz’s core strength lies in its flexible track-based system, allowing you to layer multiple types of annotations onto a single, coherent plot:

  • AxisTrack: The foundational track that displays the protein sequence as a horizontal axis, complete with numbered tick marks for easy reference. It automatically adapts to zoomed views.
  • PDBTrack: Illustrates which parts of the protein are covered by PDB structures. Offers a "full" view (each PDB entry in a separate, labelled lane) or a "collapse" view (a merged representation of all covered regions).
  • LigandInteractionTrack: Specifically designed to show residues that bind to ligands. Like PDBTrack, it supports "full" (per-ligand) and "collapse" (merged sites) plotting options.
  • TEDDomainsTrack: Visualises domain segments from the TED database, with options to display each annotation uniquely or as a merged overview.
  • AlphaFoldTrack: Dedicated to displaying AlphaFold data. It can simultaneously plot pLDDT scores (colour-coded by confidence) and average AlphaMissense pathogenicity predictions in distinct sub-tracks.
  • InterProTrack: Displays domain signatures from InterPro member databases (e.g., Pfam, CATH-Gene3D). Supports "full" mode for detailed, per-signature rows with entry type and accession labels, and "collapse" mode for a merged view.
  • CustomTrack: The most adaptable track, enabling you to plot your own data. You can define:
    • Sequence Ranges: Represent domains, motifs, or any region of interest as coloured bars.
    • Point Features: Mark specific residues (e.g., PTM sites, active site residues) using customisable markers.
    • Custom labels, colours, and grouping for each annotation.

3. Intuitive and Customisable Plotting

Protviz aims to make the creation of informative protein visualisations straightforward:

  • Unified Plotting Function: The plot_protein_tracks() function serves as the central command to combine all your defined tracks into a final figure.
  • Zoom Functionality: Easily focus on specific regions of interest by specifying view_start_aa and view_end_aa parameters, allowing for detailed examination of annotations in high-density areas.
  • Clear Labelling: Automatic and customisable labelling for tracks, axes, and individual annotations ensures that your plots are easy to understand.
  • Save and Share: Plots can be saved directly to image files (e.g., PNG) suitable for inclusion in presentations, publications, or web resources.
  • Aesthetic Control: Options for colours, bar heights, spacing, and text sizes provide control over the visual appearance of the tracks and the overall plot.

By combining these features, Protviz provides a powerful yet accessible platform for creating rich, multi-layered visualisations of protein sequence annotations.