TOPDB: Topology data bank of transmembrane proteins

Research output: Contribution to journalArticle

57 Citations (Scopus)

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.

Original languageEnglish
JournalNucleic Acids Research
Volume36
Issue numberSUPPL. 1
DOIs
Publication statusPublished - Jan 2008

Fingerprint

Databases
Proteins
Protein Databases
Internet
Names

ASJC Scopus subject areas

  • Genetics

Cite this

TOPDB : Topology data bank of transmembrane proteins. / Tusnády, G.; Kalmár, L.; Simon, I.

In: Nucleic Acids Research, Vol. 36, No. SUPPL. 1, 01.2008.

Research output: Contribution to journalArticle

@article{858874c6066f47f2bbbbcbf1662b671d,
title = "TOPDB: Topology data bank of transmembrane proteins",
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.",
author = "G. Tusn{\'a}dy and L. Kalm{\'a}r and I. Simon",
year = "2008",
month = "1",
doi = "10.1093/nar/gkm751",
language = "English",
volume = "36",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "SUPPL. 1",

}

TY - JOUR

T1 - TOPDB

T2 - Topology data bank of transmembrane proteins

AU - Tusnády, G.

AU - Kalmár, L.

AU - Simon, I.

PY - 2008/1

Y1 - 2008/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=38549172064&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=38549172064&partnerID=8YFLogxK

U2 - 10.1093/nar/gkm751

DO - 10.1093/nar/gkm751

M3 - Article

C2 - 17921502

AN - SCOPUS:38549172064

VL - 36

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - SUPPL. 1

ER -