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Protocols

TOPDB specifications

Information


Unique identifier OMICS_04184
Name TOPDB
Alternative name Topology Data Bank of Transmembrane Proteins
Restrictions to use None
Maintained Yes

Publications for Topology Data Bank of Transmembrane Proteins

TOPDB citations

 (7)
library_books

Charged residues next to transmembrane regions revisited: “Positive inside rule” is complemented by the “negative inside depletion/outside enrichment rule”

2017
BMC Biol
PMCID: 5525207
PMID: 28738801
DOI: 10.1186/s12915-017-0404-4

[…] All datasets used for analysis are listed in Table . Transmembrane protein sequences and annotations were taken from TOPDB [] and UniProt []. UniProt-derived datasets are the most comprehensive datasets, built with (1) robust transmembrane prediction methods, providing the limit of today’s achievable accuracy with r […]

library_books

Pangenome and immuno proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets

2016
BMC Genomics
PMCID: 5025611
PMID: 27634541
DOI: 10.1186/s12864-016-2951-4

[…] al proteins as cytoplasmic, extracellular, periplasmic, outer and inner membrane. Proteins located in extracellular, periplasmic and outer membranes were preferred as effective vaccine candidates []. Topology Data Bank of Transmembrane Proteins, RRID:SCR_007964 (HMMTOP) was used to predict the localization of helical trans-membrane segments and topology of transmembrane proteins []. Proteins with […]

library_books

Molecular Properties of Globin Channels and Pores: Role of Cholesterol in Ligand Binding and Movement

2016
Front Physiol
PMCID: 5011150
PMID: 27656147
DOI: 10.3389/fphys.2016.00360

[…] to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB, and TODOM data bases using the probabilistic framework of hidden Markov model (Dobson et al., ).Based on X-ray crystallography data (PDB files), Pellegrini-Calace et al. () have developed a com […]

call_split

A census of α helical membrane proteins in double stranded DNA viruses infecting bacteria and archaea

2015
BMC Bioinformatics
PMCID: 4641393
PMID: 26554846
DOI: 10.1186/s12859-015-0817-4
call_split See protocol

[…] e a statistically significant difference in the amino acid composition of 13,117 and 43 experimentally confirmed α-helical TM regions from cellular and viral proteins, respectively, obtained from the TOPDB database [] (data not shown), which demonstrates that the physico-chemical properties of these proteins are similar.To confirm the TM topology predicted by Phobius, MEMSAT3 (version 3.0) was als […]

library_books

The human transmembrane proteome

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

[…] other individually collected proteins. Here, we established a new benchmark set, comprising sequences and topologies of human TMPs only by searching sequences homologous to the human sequences in the TOPDB database. The resulting TMP set was divided into a “structure” and an “experimental” benchmark set. The former part contains human TMP sequences, whose homologues in the TOPDB database have a 3D […]

library_books

A Comprehensive Comparison of Transmembrane Domains Reveals Organelle Specific Properties

2010
Cell
PMCID: 2928124
PMID: 20603021
DOI: 10.1016/j.cell.2010.05.037

[…] al., 2007). Single-pass proteins from S. cerevisiae and H. sapiens with experimentally determined topologies and locations were identified from literature and database searches (Saccharomyces Genome, TopDB and LOCATE databases (Sprenger et al., 2008; Tusnády et al., 2008)), and grouped by subcellular location ( and ). Ortholog Identification Orthologs of each of the single-pass proteins in and […]


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TOPDB institution(s)
Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest, Hungary

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