TMVisDB Minimal Database

TMVisDB - Database Release

This is the database release accompanying the paper "TMVisDB: A Resource for Transmembrane Protein Annotations and 3D Visualizations" (2025).

Description

TMVisDB is a comprehensive SQLite database containing annotations for over 46 million predicted transmembrane proteins. The database combines AlphaFold DB structure predictions with transmembrane topology predictions from the protein language model (pLM) based method TMbed.

This release contains the core database structure and annotations, with sequence information and database indices removed due to size constraints. The full database with sequences and indices is available through the web interface at https://tmvisdb.rostlab.org.

Database Contents:

TMbed prediction

Taxonomy (Domain)

Transmembrane type

Signal Peptide

All

Bacteria

Eukaryota

Archaea

Other

Alpha-helix (TMH)

no

39,391,449

28,020,596

9,944,469

991,477

434,907

yes

4,475,707

2,977,947

1,306,796

152,801

38,163

Beta-stranded barrels (TMB)

no

323,017

269,126

43,215

1,401

9,275

yes

1,814,523

1,786,881

7,959

1,608

18,075

Both

no

20,918

16,937

3,584

90

307

yes

22,836

21,731

771

52

282

Total

46,048,450

33,093,218

11,306,794

1,147,429

501,009

Schema

The database consists of the following main tables:

organism: Contains taxonomic information

sequence: Links proteins to their organisms and UniProt identifiers

annotation: Stores transmembrane topology predictions

tminfo: Contains transmembrane statistics and classifications

A diagram of the database scheme can be found here

Note on Removed Data

To make the database distribution feasible, we removed:

All sequence information from the sequence table

All database indices (which can be recreated using the schema)

Users requiring sequence information should:

Reference the UniProt accessions provided in the database

Access the full database through our web interface

Or rebuild indices locally if needed using the schema provided in our GitHub repository

Associated Resources

Web Interface

Source Code

Database Scheme