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:

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:

1. All sequence information from the sequence table
2. All database indices (which can be recreated using the schema)

Users requiring sequence information should:

1. Reference the UniProt accessions provided in the database
2. Access the full database through our web interface
3. Or rebuild indices locally if needed using the schema provided in our GitHub repository

Associated Resources

• Web Interface
• Source Code
• Database Scheme