TOPDB


25392424	Expediting topology data gathering for the TOPDB database. [PMID: 25392424] Dobson L, Langó T, Reményi I, Tusnády GE. Abstract The Topology Data Bank of Transmembrane Proteins (TOPDB, http://topdb.enzim.ttk.mta.hu) contains experimentally determined topology data of transmembrane proteins. Recently, we have updated TOPDB from several sources and utilized a newly developed topology prediction algorithm to determine the most reliable topology using the results of experiments as constraints. In addition to collecting the experimentally determined topology data published in the last couple of years, we gathered topographies defined by the TMDET algorithm using 3D structures from the PDBTM. Results of global topology analysis of various organisms as well as topology data generated by high throughput techniques, like the sequential positions of N- or O-glycosylations were incorporated into the TOPDB database. Moreover, a new algorithm was developed to integrate scattered topology data from various publicly available databases and a new method was introduced to measure the reliability of predicted topologies. We show that reliability values highly correlate with the per protein topology accuracy of the utilized prediction method. Altogether, more than 52,000 new topology data and more than 2600 new transmembrane proteins have been collected since the last public release of the TOPDB database. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2015:43(Database issue) \| 23 Citations (from Europe PMC, 2025-03-29)
17921502	TOPDB: topology data bank of transmembrane proteins. [PMID: 17921502] Tusnády GE, Kalmár L, Simon I. Abstract 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. Nucleic Acids Res. 2008:36(Database issue) \| 47 Citations (from Europe PMC, 2025-03-29)

Expediting topology data gathering for the TOPDB database. [PMID: 25392424]

Dobson L, Langó T, Reményi I, Tusnády GE.

The Topology Data Bank of Transmembrane Proteins (TOPDB, http://topdb.enzim.ttk.mta.hu) contains experimentally determined topology data of transmembrane proteins. Recently, we have updated TOPDB from several sources and utilized a newly developed topology prediction algorithm to determine the most reliable topology using the results of experiments as constraints. In addition to collecting the experimentally determined topology data published in the last couple of years, we gathered topographies defined by the TMDET algorithm using 3D structures from the PDBTM. Results of global topology analysis of various organisms as well as topology data generated by high throughput techniques, like the sequential positions of N- or O-glycosylations were incorporated into the TOPDB database. Moreover, a new algorithm was developed to integrate scattered topology data from various publicly available databases and a new method was introduced to measure the reliability of predicted topologies. We show that reliability values highly correlate with the per protein topology accuracy of the utilized prediction method. Altogether, more than 52,000 new topology data and more than 2600 new transmembrane proteins have been collected since the last public release of the TOPDB database. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 23 Citations (from Europe PMC, 2025-03-29)

TOPDB: topology data bank of transmembrane proteins. [PMID: 17921502]

Tusnády GE, Kalmár L, Simon I.

Abstract

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.

Nucleic Acids Res. 2008:36(Database issue) | 47 Citations (from Europe PMC, 2025-03-29)

URL:	http://topdb.enzim.hu
Full name:	Topology Database of Transmembrane Proteins
Description:	TOPDB is currently the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information.
Year founded:	2008
Last update:	2014-09-05
Version:
Accessibility:	Accessible
Country/Region:	Hungary

Data type:	Protein
Data object:	Animal Bacteria Plant
Database category:	Structure
Major species:	Bacillus subtilis Bos taurus Arabidopsis thaliana Caenorhabditis elegans Zea mays
Keywords:	topology prediction algorithm transmembrane protein

University/Institution:	Institute of Enzymology, Hungarian Academy of Sciences
Address:	'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518, Hungary
City:	Budapest
Province/State:
Country/Region:	Hungary
Contact name (PI/Team):	Administrator
Contact email (PI/Helpdesk):	topdb@enzim.hu

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