Nucleic Acids Research Advance Access originally published online on October 5, 2007
Nucleic Acids Research 2008 36(Database issue):D234-D239; doi:10.1093/nar/gkm751
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Nucleic Acids Research, 2008, Vol. 36, Database issue D234-D239
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
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TOPDB: topology data bank of transmembrane proteins
Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary
*To whom correspondence should be addressed. Tel: +36 1 466 9276; Fax: +36 1 466 5465; Email: tusi{at}enzim.hu
Received August 8, 2007. Revised September 3, 2007. Accepted September 10, 2007.
The Topology Data Bank of Transmembrane Proteins (TOPDB) is the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information currently available. It contains information gathered from the literature and from public databases available on the internet for more than a thousand transmembrane proteins. TOPDB collects details of various experiments that were carried out to learn about the topology of particular transmembrane proteins. In addition to experimental data from the literature, an extensive collection of structural data was also compiled from PDB and from PDBTM. Because topology information is often incomplete, for each protein in the database the most probable topology that is consistent with the collected experimental constraints was also calculated using the HMMTOP transmembrane topology prediction algorithm. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. The web interface of TOPDB includes tools for searching, relational querying and data browsing as well as for visualization. TOPDB is designed to bridge the gap between the number of transmembrane proteins available in sequence databases and the publicly accessible topology information of experimentally or computationally studied transmembrane proteins. TOPDB is available at http://topdb.enzim.hu.
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