TMVisDB

A database for searching and visualizing predicted transmembrane proteins with their AlphaFold structures. 🦭

Overview

TMvisDB provides per-residue transmembrane topology annotations for all proteins in AlphaFold DB (~ 200 million proteins, September '22) predicted as transmembrane proteins (~ 46 million). The annotations are predicted using TMbed and visualized by overlaying them with AlphaFold 2 structures.

The web interface is accessible here

Preview

Figure caption

3D structure and membrane topology visualization protein DnaJ homolog subfamily C member 11 (Q9NVH1). The protein DnaJ with per-residue topology color-scheme: inside-to-outside TMH (light red), outside-to-inside TMH (dark red), inside-to-outside TMB (light blue), outside-to-inside TMB (dark blue),other (grey). The length of the alpha-helix and beta-barrel could align with membrane boundaries.

Features

• Protein Search: Search for specific proteins using UniProt identifiers
• Advanced Filtering: Filter proteins by:
  • Transmembrane topology (alpha-helix, beta-strand)
  • Signal peptide presence
  • Taxonomy (UniProt Organism ID, Domain, Kingdom)
  • Protein length
• 3D Visualization: Interactive visualization of:
  • Protein structures from AlphaFold DB
  • Transmembrane topology annotations
  • pLDDT confidence scores
• Multiple Data Sources: Integration with:
  • TMbed predictions
  • AlphaFold DB structures (~200M proteins)
  • UniProt annotations
  • TopDB experimental data
  • TMAlphaFold annotations
  • Membranome annotations
  • LambdaPP protein-specific phenotype predictions
  • Foldseek structural alignments

Technology Stack

Frontend

• SvelteKit
• TanStack Query
• Skeleton UI
• TypeScript

Backend

• FastAPI
• SQLModel
• Python 3.12+
• SQLite

Development

Prerequisites

• Node.js
• Python 3.12+
• pnpm (recommended)

Setup

1. Clone the repository:

   git clone https://github.com/t03i/tmvisdb.git
   cd tmvisdb

2. Install frontend dependencies:

   cd frontend
   pnpm install

3. Start the development server:

   Frontend:

   cd frontend
   pnpm dev

   Backend:

   docker compose -f docker-compose.yaml -f docker-compose.dev.yaml up -d

Citations

If you use TMvisDB in your research, please cite:

@article{tmvisdb2024,
title={TMvisDB: A database for visualization of predicted transmembrane proteins},
author={...},
journal={bioRxiv},
year={2022},
doi={10.1101/2022.11.30.518551}
}

For predicted annotations in the database:

• TMbed: DOI: 10.1186/s12859-022-04873-x

For structures:

• AlphaFold DB: DOI: 10.1093/nar/gkab1061
• AlphaFold: DOI: 10.1038/s41586-021-03819-2

Additional tools and resources:

• Membranome:
  • DOI: 10.1093/nar/gkw712
  • DOI: 10.1093/bioinformatics/btx720
  • Website: https://membranome.org/
• TMAlphaFold:
  • DOI: 10.1093/nar/gkac928
  • Website: https://tmalphafold.ttk.hu/
• TopDB:
  • DOI: 10.1093/nar/gkad897
  • DOI: 10.1093/nar/gku1119
  • DOI: 10.1093/nar/gkm751
  • Website: http://topdb.enzim.hu/
• Uniprot:
  • DOI: 10.1093/nar/gkac1052
  • Website: https://www.uniprot.org/

License

Apache-2.0 License - see LICENSE for details

Resources

• Issue Tracker
• Discussions
• Code of Conduct

Acknowledgments

Developed and maintained at Rostlab