The Topology Data Bank of Transmembrane Proteins (TOPDB) is currently the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information. It contains records for 5678 transmembrane proteins with information gathered from the literature and from public databases available on the World Wide Web.
The database collects the details of various experiments carried out to learn about the topology of particular transmembrane proteins. The experimental techniques include fusion with reporter enzymes, glycolysation studies, protease accessibility, immunolocalisation, etc. In addition to literature-derived data, an extensive collection of structural data was also compiled from Protein Data Bank (PDB) and from Protein Data Bank of Transmembrane Proteins (PDBTM) by utilising the TMDET algorithm.
While literature-derived data can not be collected automatically, data based on 3D structures provides semi-automatic and continuously updated information for the database. Structural data is the most reliable information about transmembrane topologies, but the topology information is often incomplete. Therefore, for each protein in the database the most probable topology consistent with the collected experimental constraints was also calculated using CCTOP transmembrane topology prediction algorithms for α-helical and β-barrel transmembrane proteins, respectively.
Each record in TOPDB also contains the indispensable information about the given protein such as its sequence, name, organism and cross references to various databases ( PDB, PDBTM, UniProt and literature references from PubMed).
This web interface of TOPDB includes tools for extensive searching (top bar), data browsing as well as provides visualisation tools for topology data.
The TOPDB is designed to address the broad gap between the large number of transmembrane proteins in sequence databases and the publicly available topology information of experimentally or computationally studied transmembrane proteins.
- Dobson L, Gerdán C, Tusnády S, Langó T, Zeke A, Szekeres L, Kuffa K and Tusnády GE (2024)
UniTmp: Unified resources for transmembrane proteins.
Nucleic Acids Research submitted,
- Dobson L, Langó T, Reményi I and Tusnády GE (2015)
Expediting topology data gathering for the TOPDB database.
Nucleic Acids Research 43, D283-9.
[Journal] [PubMed] [PDF]
- Tusnády GE, Kalmár L and Simon I (2008)
TOPDB: Topology Data Bank of Transmembrane Proteins.
Nucleic Acids Research 36, D234-9.
[Journal] [PubMed] [PDF]