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TOPDOM specifications

Information


Unique identifier OMICS_12725
Name TOPDOM
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.003
Maintained Yes

Maintainer


  • person_outline Gabor Tusnady

Publications for TOPDOM

TOPDOM citations

 (3)
library_books

The human transmembrane proteome

2015
Biol Direct
PMCID: 4445273
PMID: 26018427
DOI: 10.1186/s13062-015-0061-x

[…] evidence level is the Experiment level, when the 3D structures of the protein itself or of homologous proteins are not known, but some molecular biology experiments were made. Entries are marked with TOPDOM evidence level, if bioinformatic evidences can be found that can be used as a strong argument to define the topology of the full protein or some parts of it. The experimental topology data is c […]

library_books

Reptation Induced Coalescence of Tunnels and Cavities in Escherichia Coli XylE Transporter Conformers Accounts for Facilitated Diffusion

2014
PMCID: 4207944
PMID: 25163893
DOI: 10.1007/s00232-014-9711-7

[…] amino acids A, G, P, V, or C to produce the distributions. The EMBOSS utility ‘Shuffleseq’ generated the randomised sets of data. Similar searches were done in the database for transmembrane proteins TOPDOM. http://topdom.enzim.hu. (Tusnády et al. ). […]

library_books

Structural fragment clustering reveals novel structural and functional motifs in α helical transmembrane proteins

2010
BMC Bioinformatics
PMCID: 2876129
PMID: 20420672
DOI: 10.1186/1471-2105-11-204

[…] embrane proteins. There are no comprehensive studies, to our knowledge, that focus on functional/structural motifs in transmembrane proteins. Among recent studies on transmembrane protein motifs, the TOPDOM database [] collects domains and transmembrane protein sequence motifs from different motif databases and organizes them by their location in the protein with respect to the lipid layer.In the […]

Citations

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TOPDOM institution(s)
‘Momentum’ Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest, Hungary
TOPDOM funding source(s)
This work was supported by grants from Hungarian Research and Developments Fund [OTKA K104586] and the Momentum Grant of Hungarian Academy of Science [LP2012-35].

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