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NLSdb specifications

Information


Unique identifier OMICS_18460
Name NLSdb
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline Michael Bernhofer

Publications for NLSdb

NLSdb citations

 (5)
library_books

The molecular mechanism for nuclear transport and its application

2017
PMCID: 5509903
PMID: 28713609
DOI: 10.5115/acb.2017.50.2.77

[…] g.Many researchers have tried to develop ideal drug delivery systems by using modification of NLSs []. Based on previous results, several bioinformatic tools, such as NucPred, NLS Mapper, NESbase and NLSdb, have been developed about subcellular localization of proteins []. Using these tools, we can search the subcellular locations of targeting molecules. More importantly, users can predict subcell […]

library_books

Bioinformatic and mass spectrometry identification of Anaplasma phagocytophilum proteins translocated into host cell nuclei

2015
Front Microbiol
PMCID: 4319465
PMID: 25705208
DOI: 10.3389/fmicb.2015.00055

[…] a poorly studied signal that is not incorporated in most NLS prediction algorithms. To screen broadly for potential NLSs, we selected MultiLoc (Hoglund et al., ). MultiLoc also identifies matches in NLSdb, a database of experimentally known NLSs (Nair et al., ) and is also useful to predict NLSm and NLSb in addition to the NLSdb attribute, since NLSdb recognizes only 43% of the nuclear proteins. […]

library_books

Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing

2012
BMC Bioinformatics
PMCID: 3521467
PMID: 23282098
DOI: 10.1186/1471-2105-13-S17-S13

[…] edictors are designed specifically to identify proteins imported into the nucleus. PredictNLS [] predicts nuclear proteins based on the presence of known or putative NLSs derived from the contents of NLSdb. NucPred [] uses regular expression matching and multiple program classifiers induced by genetic programming to detect putative NLSs. NUCLEO [] incorporates sequence motifs from known NLSs in a […]

library_books

The proteins of intra nuclear bodies: a data driven analysis of sequence, interaction and expression

2010
BMC Syst Biol
PMCID: 2859750
PMID: 20388198
DOI: 10.1186/1752-0509-4-44

[…] ns to enter the nucleus but not the only one. To explore the effect of NLS on intra-nuclear sorting, we identify NLS-carrying nuclear proteins by matching the amino acid sequence to the 312 motifs in NLSdb []. Bickmore and Surtherland [] report that by using PSORT they detect NLS in 80-86% proteins that localize to nucleoli, nuclear speckles and PML nuclear bodies; and 62% of proteins that associa […]

library_books

The obesity gene, TMEM18, is of ancient origin, found in majority of neuronal cells in all major brain regions and associated with obesity in severely obese children

2010
BMC Med Genet
PMCID: 2858727
PMID: 20380707
DOI: 10.1186/1471-2350-11-58

[…] ters. Phosphorylation sites were predicted with the NetPhos [] (v. 2.0) server using the default parameters. The prediction of nuclear localization signals (NLS) was performed with PredictNLS and the NLSdb database []. Finally, the UniProt and Ensembl websites were consulted for additional annotation. […]

Citations

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NLSdb institution(s)
Department of Informatics, I12-Chair of Bioinformatics and Computational Biology, Technical University of Munich (TUM), Garching/Munich, Germany; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QSL, Australia; Institute of Advanced Study (TUM-IAS), Garching/Munich, Germany; Institute for Food and Plant Sciences WZW-Weihenstephan, Freising, Germany; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
NLSdb funding source(s)
Supported by Alexander von Humboldt Foundation through German Federal Ministry for Education and Research; Bavarian Competence Network for Technical and Scientific High Performance Computing (KONWIHR-III); Ernst Ludwig Ehrlich Studienwerk.

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