TOPDB: Topology Database of Transmembrane Proteins

About TOPDB

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 4190 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 and HMMTOP 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, relational querying and data browsing as well as 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.

Manuscripts

Tusnády GE, Kalmár L and Simon I (2008)

TOPDB: Topology Data Bank of Transmembrane Proteins.

Nucleic Acids Research 36 Database issue, D234-D239.

[Journal] [Medline] [PDF]

Dobson L, Langó T, Reményi I and Tusnády GE (2015)

Expediting topology data gathering for the TOPDB database.

Nucleic Acids Research 43 Database issue, D283-D289.

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Related manuscripts

Gardy JL, Spencer C, Wang K, Ester M, Tusnády GE, Simon I, Hua S, deFays K, Lambert C, Nakai K and Brinkman FS (2003)

PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria.

Nucleic Acids Res 31, 3613-3617.

[Journal] [Medline] [PDF] [Server]

Dosztányi Zs, Magyar Cs, Tusnády GE, Cserző M, Fiser A and Simon I (2003)

Servers for sequence-structure relationship analysis and prediction.

Nucleic Acids Res 31, 3359-3363.

[Journal] [Medline] [PDF] [Servers]

Tusnády GE, Dosztányi Zs and Simon I (2004)

Transmembrane proteins in protein data bank: identification and classification.

Bioinformatics 20, 2964-2972.

[Journal] [Medline] [PDF] [Server]

Tusnády GE, Dosztányi Zs and Simon I (2004)

TMDET: web server for detecting transmembrane domains by using 3D structure of proteins

Bioinformatics 21, 1276-7.

[Journal] [Medline] [PDF] [Server]

Tusnády GE, Dosztányi Zs and Simon I (2005)

PDB_TM: selection and membrane localization of transmembrane proteins in the Protein Data Bank.

Nucleic Acids Research 33 Database Issue, D275-D278.

[Journal] [Medline] [PDF] [Server]

Tusnády GE, Kalmár L, Hegyi H, Tompa P and Simon I. (2008)

TOPDOM: database of domains and motifs with conservative location in transmembrane proteins.

Bioinformatics 24, 1469-70.

[Journal] [Medline] [PDF] [Server]