R34M07 last accessed: 2022-11-04

glycomedb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.412261

Other names: A carbohydrate structure metadatabase, glycomedb

GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.

Webpage:

http://www.glycome-db.org/showMenu.action?major=database

Licence:

Name: Copyrights
URL: http://www.glycome-db.org/index.html

Publications:

Publications
More detailed information about this field from each metasource.

GlycomeDB--a unified database for carbohydrate structures
PMID: 21045056
metasource: Fairsharing.org
version: FAIRsharing.org: GlycomeDB; GlycomeDB; DOI: https://doi.org/10.25504/FAIRsharing.k5k0yh; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.412261

GlycomeDB - integration of open-access carbohydrate structure databases
PMID: 18803830
metasource: Fairsharing.org
version: FAIRsharing.org: GlycomeDB; GlycomeDB; DOI: https://doi.org/10.25504/FAIRsharing.k5k0yh; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences
PMID: 19759275
metasource: Fairsharing.org
version: FAIRsharing.org: GlycomeDB; GlycomeDB; DOI: https://doi.org/10.25504/FAIRsharing.k5k0yh; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

http://nar.oxfordjournals.org/content/39/suppl_1/D373
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

GlycomeDB--a unified database for carbohydrate structures PubMed citations: 46.

46 articles citing: GlycomeDB--a unified database for carbohydrate structures

Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3. PMID:34824474
Glycoinformatics Tools for Comprehensive Characterization of Glycans Enzymatically Released from Proteins. PMID:34611862
Proteogenomic characterization of pancreatic ductal adenocarcinoma. PMID:34534465
FGDB: Database of follicle stimulating hormone glycans. PMID:33897975
The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application. PMID:33677548
Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy. PMID:33302373
Glycoproteomics-based signatures for tumor subtyping and clinical outcome prediction of high-grade serous ovarian cancer. PMID:33262351
Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma. PMID:33086064
Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics. PMID:32937895
Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search. PMID:32102970
GRITS Toolbox-a freely available software for processing, annotating and archiving glycomics mass spectrometry data. PMID:30913289
N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search. PMID:30186849
Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides. PMID:29741879
Comparison of Collisional and Electron-Based Dissociation Modes for Middle-Down Analysis of Multiply Glycosylated Peptides. PMID:29663256
Glycoengineering of Mammalian Expression Systems on a Cellular Level. PMID:29532110
GLYDE-II: The GLYcan data exchange format. PMID:28955652
High-throughput analysis of N-glycans using AutoTip via glycoprotein immobilization. PMID:28860471
An editor for the generation and customization of geometry restraints. PMID:28177308
Classification of Tandem Mass Spectra for Identification of N- and O-linked Glycopeptides. PMID:27869200
Modulating carbohydrate-protein interactions through glycoengineering of monoclonal antibodies to impact cancer physiology. PMID:27639240
A systematic framework to derive N-glycan biosynthesis process and the automated construction of glycosylation networks. PMID:27454116
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. PMID:27296299
pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD- and CID-MS/MS and MS3. PMID:27139140
MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification. PMID:27084943
Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions. PMID:26984886
Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search. PMID:26656740
SugarBindDB, a resource of glycan-mediated host-pathogen interactions. PMID:26578555
GlyTouCan 1.0--The international glycan structure repository. PMID:26476458
Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts. PMID:26286194
Implementation of linked data in the life sciences at BioHackathon 2011. PMID:25973165
Integration of systems glycobiology with bioinformatics toolboxes, glycoinformatics resources, and glycoproteomics data. PMID:25871730
Alterations in the proteome of the respiratory tract in response to single and multiple exposures to naphthalene. PMID:25825134
High-Throughput Analysis and Automation for Glycomics Studies. PMID:25814696
Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins. PMID:25108191
PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins. PMID:24857970
Glycoproteomic and glycomic databases. PMID:24725457
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. PMID:24495517
Introducing glycomics data into the Semantic Web. PMID:24280648
Correct primary structure assessment and extensive glyco-profiling of cetuximab by a combination of intact, middle-up, middle-down and bottom-up ESI and MALDI mass spectrometry techniques. PMID:23924801
Using databases and web resources for glycomics research. PMID:23325765
Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology. PMID:23230149
Alteration of the serum N-glycome of mice locally exposed to high doses of ionizing radiation. PMID:23146835
The use of glycoinformatics in glycochemistry. PMID:23015842
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
Novel data analysis tool for semiquantitative LC-MS-MS2 profiling of N-glycans. PMID:22707226
Bioinformatics and systems biology of the lipidome. PMID:21939287
GlycomeDB - integration of open-access carbohydrate structure databases PubMed citations: 34.

34 articles citing: GlycomeDB - integration of open-access carbohydrate structure databases

Informatics Ecosystems to Advance the Biology of Glycans. PMID:34626414
Glycosylation Biomarkers Associated with Age-Related Diseases and Current Methods for Glycan Analysis. PMID:34071388
Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy. PMID:33302373
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer. PMID:33093930
Three-Dimensional Structures of Carbohydrates and Where to Find Them. PMID:33081008
Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics. PMID:32937895
Towards a standardized bioinformatics infrastructure for N- and O-glycomics. PMID:31332201
GRITS Toolbox-a freely available software for processing, annotating and archiving glycomics mass spectrometry data. PMID:30913289
GlycanFormatConverter: a conversion tool for translating the complexities of glycans. PMID:30535258
The Glycoscience of Immunity. PMID:29759949
Emerging glycobiology tools: A renaissance in accessibility. PMID:29759530
Comparison of Collisional and Electron-Based Dissociation Modes for Middle-Down Analysis of Multiply Glycosylated Peptides. PMID:29663256
GlyTouCan: an accessible glycan structure repository. PMID:28922742
A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry. PMID:28337402
Gly-Spec: a webtool for predicting glycan specificity by integrating glycan array screening data and 3D structure. PMID:28120784
Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions. PMID:26984886
GlycoRDF: an ontology to standardize glycomics data in RDF. PMID:25388145
Qrator: a web-based curation tool for glycan structures. PMID:25165068
Site-specific glycan microheterogeneity of inter-alpha-trypsin inhibitor heavy chain H4. PMID:24884609
Glycoproteomic and glycomic databases. PMID:24725457
Toolboxes for a standardised and systematic study of glycans. PMID:24564482
Exploring site-specific N-glycosylation microheterogeneity of haptoglobin using glycopeptide CID tandem mass spectra and glycan database search. PMID:23829323
Computational screening of the human TF-glycome provides a structural definition for the specificity of anti-tumor antibody JAA-F11. PMID:23365681
Software tools for glycan profiling. PMID:23296537
Software for automated interpretation of mass spectrometry data from glycans and glycopeptides. PMID:23293784
The use of glycoinformatics in glycochemistry. PMID:23015842
Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC-MS/MS, and glycan database search. PMID:22239659
SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds. PMID:21992011
The annotation of the asparagine N-linked glycosylation pathway in the Reactome database. PMID:21199820
Recent advances in the MS analysis of glycoproteins: Capillary and microfluidic workflows. PMID:21171110
EUROCarbDB: An open-access platform for glycoinformatics. PMID:21106561
GlycomeDB--a unified database for carbohydrate structures. PMID:21045056
GlycoViewer: a tool for visual summary and comparative analysis of the glycome. PMID:20501599
Bioinformatics and molecular modeling in glycobiology. PMID:20364395
Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences PubMed citations: 25.

25 articles citing: Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences

gQuant, an Automated Tool for Quantitative Glycomic Data Analysis. PMID:34395380
Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy. PMID:33302373
Three-Dimensional Structures of Carbohydrates and Where to Find Them. PMID:33081008
Glycosaminoglycanomics: where we are. PMID:27900575
Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules. PMID:27549814
A review of methods for interpretation of glycopeptide tandem mass spectral data. PMID:26612686
GlycoMob: an ion mobility-mass spectrometry collision cross section database for glycomics. PMID:26314736
GlycoRDF: an ontology to standardize glycomics data in RDF. PMID:25388145
Qrator: a web-based curation tool for glycan structures. PMID:25165068
Site-specific glycan microheterogeneity of inter-alpha-trypsin inhibitor heavy chain H4. PMID:24884609
Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010. PMID:24863367
Toolboxes for a standardised and systematic study of glycans. PMID:24564482
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. PMID:24495517
A general strategy for the chemoenzymatic synthesis of asymmetrically branched N-glycans. PMID:23888036
Exploring site-specific N-glycosylation microheterogeneity of haptoglobin using glycopeptide CID tandem mass spectra and glycan database search. PMID:23829323
The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics. PMID:23271684
The use of glycoinformatics in glycochemistry. PMID:23015842
Glycan fingerprints: calculating diversity in glycan libraries. PMID:22373368
GlycomicsDB - A Data Integration Platform for Glycans and their Strucutres. PMID:21603090
Systems glycobiology: biochemical reaction networks regulating glycan structure and function. PMID:21436236
The annotation of the asparagine N-linked glycosylation pathway in the Reactome database. PMID:21199820
EUROCarbDB: An open-access platform for glycoinformatics. PMID:21106561
GlycomeDB--a unified database for carbohydrate structures. PMID:21045056
SuperSweet--a resource on natural and artificial sweetening agents. PMID:20952410
Bioinformatics and molecular modeling in glycobiology. PMID:20364395
http://nar.oxfordjournals.org/content/39/suppl_1/D373

Tags:

Tags
More detailed information about this field from each metasource.

carbohydrate
metasource: Fairsharing.org
version: FAIRsharing.org: GlycomeDB; GlycomeDB; DOI: https://doi.org/10.25504/FAIRsharing.k5k0yh; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: re3data.org
version: re3data.org: GlycomeDB; editing status 2021-07-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34M07 last accessed: 2022-11-04

molecular entity
metasource: Fairsharing.org
version: FAIRsharing.org: GlycomeDB; GlycomeDB; DOI: https://doi.org/10.25504/FAIRsharing.k5k0yh; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: GlycomeDB; GlycomeDB; DOI: https://doi.org/10.25504/FAIRsharing.k5k0yh; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: GlycomeDB; GlycomeDB; DOI: https://doi.org/10.25504/FAIRsharing.k5k0yh; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

structure
metasource: Fairsharing.org
version: FAIRsharing.org: GlycomeDB; GlycomeDB; DOI: https://doi.org/10.25504/FAIRsharing.k5k0yh; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

carbohydrates
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.412261

glycobiology
metasource: re3data.org
version: re3data.org: GlycomeDB; editing status 2021-07-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R34M07 last accessed: 2022-11-04

proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.412261

structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.412261

data submission, annotation and curation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.412261

carbohydrate molecular entity molecular structure small molecule structure structure carbohydrates glycobiology proteins structure analysis data submission, annotation and curation

More to explore:

1/20

Previous Next

Need help integrating and/or managing biomedical data?

Webpage:

Licence:

More to explore:

1/20

CCSD - Complex Carbohydrate Structure Database (CarbBank)

CSS - Carbohydrate Structure Suite

Web3 Unique Representation of Carbohydrate Structures

Carbohydrate Structure Database

Bacterial CSDB (BCSDB)

Glycosciences.de DB

PFCSDB

Molecular Modeling Database

The Carbohydrate-Active enZYmes Database

PDBsum; at-a-glance overview of macromolecular structures

GlyTouCan

Glycan

Worldwide Protein Data Bank

Protein Data Bank in Europe

Jenalib: Jena Library of Biological Macromolecules

RCSB Protein Data Bank

EuroCarbDB

Protein Data Bank Japan

Structural Classification Of Proteins

Manually Curated Database of Rice Proteins