O-GlycBase statistics

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O-GlycBase specifications

Information


Unique identifier OMICS_02424
Name O-GlycBase
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Ramneek Gupta

Publication for O-GlycBase

O-GlycBase citations

 (6)
library_books

GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N linked and O linked glycoproteomes by incorporating structural features

2016
Sci Rep
PMCID: 5052564
PMID: 27708373
DOI: 10.1038/srep34595

[…] The annotations of C-, N-, and O-linked glycosylation sites were extracted from four major public resources, including UniProt, PhosphoSitePlus, SysPTM, and O-GlycBase (version 6.0). Only experimentally verified glycosylation sites in the human proteins were retained. To ensure the quality of the curated datasets, any glycosylation sites annotated as “Pro […]

library_books

Characterization and identification of protein O GlcNAcylation sites with substrate specificity

2014
BMC Bioinformatics
PMCID: 4290634
PMID: 25521204
DOI: 10.1186/1471-2105-15-S16-S1

[…] The experimentally verified O-GlcNAcylation sites were mainly extracted from dbPTM [-] which have integrated several protein glycosylation-associated databases: dbOGAP [], UniProtKB [], O-GlycBase [], and PhosphoSitePlus []. The dbOGAP database contains 240 and 135 sites for O-GlcNAcylated serine (Ser) and threonine (Thr) on 168 proteins. O-GlcNAcylation data, from UniProtKB, that ar […]

library_books

Human germline and pan cancer variomes and their distinct functional profiles

2014
Nucleic Acids Res
PMCID: 4191387
PMID: 25232094
DOI: 10.1093/nar/gku772

[…] compilation of publicly available databases and generates a data set containing only experimentally verified entries, which include data from UniProtKB/Swiss-Prot, Phospho.ELM (), PhosphoSitePlus (), O-GLYCBASE (), dbSNO (), SysPTM () and HPRD (). However, heterogeneity issues still left unresolved include (i) annotations are not mapped to a unified proteome reference and (ii) naming of PTMs is no […]

library_books

Bioinformatics and molecular modeling in glycobiology

2010
PMCID: 2912727
PMID: 20364395
DOI: 10.1007/s00018-010-0352-4

[…] predication tool, uses a hybrid combinatorial and statistical learning approach based on random forests. Training datasets for the statistical learning approaches are usually derived from the PDB or O-GLYCBASE [].The mechanism of acceptor site selection for the covalent attachment of carbohydrates by a series of glycosyl transferases in the case of C-type and O-type glycosylation, and by the olig […]

library_books

A comprehensive resource for integrating and displaying protein post translational modifications

2009
BMC Res Notes
PMCID: 2713254
PMID: 19549291
DOI: 10.1186/1756-0500-2-111

[…] tional identification of PTMs, and the structural and functional annotations of PTMs. We integrated five PTM databases, including UniProtKB/Swiss-Prot (release 55.0) [], Phospho.ELM (version 7.0) [], O-GLYCBASE (version 6.0) [], UbiProt (version 1.0) [] and PHOSIDA (version 1.0) [] for obtaining experimental protein modifications. The description and data statistics of these databases are briefly […]

library_books

Creation and disruption of protein features by alternative splicing a novel mechanism to modulate function

2005
Genome Biol
PMCID: 1175989
PMID: 15998447
DOI: 10.1186/gb-2005-6-7-r58

[…] s residue is close to an exon boundary, an alternative splice event can change the context to an unfavorable one with the consequence that the modification cannot take place anymore. We inspected the O-GlycBase [] and Phospho.ELM [], and found 435 modified residues that are close to 213 different exon-exon junctions. Among them, four exon junctions showed an insert due to alternative splicing. CCL […]

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O-GlycBase institution(s)
Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby, Denmark

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