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Protocols

NESbase specifications

Information


Unique identifier OMICS_05912
Name NESbase
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Ramneek Gupta

Publication for NESbase

NESbase 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

[…] ear targeting.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 pre […]

library_books

Sequence and structural analyses of nuclear export signals in the NESdb database

2012
Mol Biol Cell
PMCID: 3442415
PMID: 22833565
DOI: 10.1091/mbc.E12-01-0046

[…] real from false-positive NESs and to improve prediction efforts in the future.la , ) made the first attempt to systematically analyze NES properties of 67 NESs that were collected in a database named NESbase. Their study revealed interesting NES properties, such as overrepresentation of acidic residues in nonhydrophobic positions of NESs, preference for α-helical structure, and tendency of NESs to […]

library_books

Nucleocytoplasmic Shuttling Activity of Ataxin 3

2009
PLoS One
PMCID: 2688764
PMID: 19503814
DOI: 10.1371/journal.pone.0005834

[…] dentified by consensus to the ΦX1–3ΦX2–3ΦXΦ motif (Φ indicates a large hydrophobic residue, and X indicates any amino acid), and using the prediction algorithm NetNES (http://www.cbs.dtu.dk/databases/NESbase-1.0 ), and fused to Rev(1.4)-GFP fusion protein (the plasmid encoding Rev(1.4)-GFP was kindly provided by Beric R. Henderson). The putative sequences that were assayed include: NES1, residues […]

library_books

Identification and characterization of human Mex 3 proteins, a novel family of evolutionarily conserved RNA binding proteins differentially localized to processing bodies

2007
Nucleic Acids Res
PMCID: 1851655
PMID: 17267406
DOI: 10.1093/nar/gkm016

[…] ml) (). Potential structural protein domains were predicted by SMART (http://dylan.embl-heidelberg.de/) () and PSORT (http://psort.nibb.ac.jp/) (). Consensus sequence L-x(,)-[LIVFM-x(,)-L-x-[LI] from NESbase (http://www.cbs.dtu.dk/databases/NESbase-1.0/) () was used to predict NES sequence localization. Amino acid sequences were aligned by ClustalW (http://www.ebi.ac.uk/clustalw/) () and T-coffee […]

call_split

Identification of a novel Rev interacting cellular protein

2005
BMC Cell Biol
PMCID: 1097722
PMID: 15847701
DOI: 10.1186/1471-2121-6-20
call_split See protocol

[…] tion and analysis of sequences were performed using the databases and bioinformatics tools of NCBI [] and of Genomatix Software GmbH [].Similarities between nuclear export signals in the NES database NESbase 1.0 [] were analysed with a set of amino acid weight matrices adapted from the MatInspector algorithm [] using the BLOSSOM similarity matrix values to account for conserved amino acid substitu […]

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NESbase institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

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