TOPDOM


27153630	TOPDOM: database of conservatively located domains and motifs in proteins. [PMID: 27153630] Varga J, Dobson L, Tusnády GE. Abstract The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in ?-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. Bioinformatics. 2016:32(17) \| 3 Citations (from Europe PMC, 2025-03-15)
18434342	TOPDOM: database of domains and motifs with conservative location in transmembrane proteins. [PMID: 18434342] Tusnády GE, Kalmár L, Hegyi H, Tompa P, Simon I. Abstract The TOPDOM database is a collection of domains and sequence motifs located consistently on the same side of the membrane in alpha-helical transmembrane proteins. The database was created by scanning well-annotated transmembrane protein sequences in the UniProt database by specific domain or motif detecting algorithms. The identified domains or motifs were added to the database if they were uniformly annotated on the same side of the membrane of the various proteins in the UniProt database. The information about the location of the collected domains and motifs can be incorporated into constrained topology prediction algorithms, like HMMTOP, increasing the prediction accuracy. The TOPDOM database and the constrained HMMTOP prediction server are available on the page http://topdom.enzim.hu tusi@enzim.hu; lkalmar@enzim.hu. Bioinformatics. 2008:24(12) \| 16 Citations (from Europe PMC, 2025-03-15)

TOPDOM: database of conservatively located domains and motifs in proteins. [PMID: 27153630]

Varga J, Dobson L, Tusnády GE.

The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in ?-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Bioinformatics. 2016:32(17) | 3 Citations (from Europe PMC, 2025-03-15)

TOPDOM: database of domains and motifs with conservative location in transmembrane proteins. [PMID: 18434342]

Tusnády GE, Kalmár L, Hegyi H, Tompa P, Simon I.

Abstract

The TOPDOM database is a collection of domains and sequence motifs located consistently on the same side of the membrane in alpha-helical transmembrane proteins. The database was created by scanning well-annotated transmembrane protein sequences in the UniProt database by specific domain or motif detecting algorithms. The identified domains or motifs were added to the database if they were uniformly annotated on the same side of the membrane of the various proteins in the UniProt database. The information about the location of the collected domains and motifs can be incorporated into constrained topology prediction algorithms, like HMMTOP, increasing the prediction accuracy. The TOPDOM database and the constrained HMMTOP prediction server are available on the page http://topdom.enzim.hu tusi@enzim.hu; lkalmar@enzim.hu.

Bioinformatics. 2008:24(12) | 16 Citations (from Europe PMC, 2025-03-15)

URL:	http://topdom.enzim.hu/
Full name:	database of conservatively located domains and motifs in proteins
Description:	a collection of domains and sequence motifs located conservatively in one side of membranes either in transmembrane or globular proteins
Year founded:	2008
Last update:	2016-05-23
Version:	v 2.003
Accessibility:	Accessible
Country/Region:	Hungary

Data type:	Protein
Data object:	NA
Database category:	Structure
Major species:	NA
Keywords:	membrane protein protein domain protein motif

University/Institution:	Institute of Enzymology, Hungarian Academy of Sciences
Address:	'Momentum' Membrane Protein Bioinformatics Research Group
City:	Budapest
Province/State:
Country/Region:	Hungary
Contact name (PI/Team):	Gábor E. Tusnády
Contact email (PI/Helpdesk):	tusnady.gabor@ttk.mta.hu

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Database Commons a catalog of worldwide biological databases