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Glycomic databases | Metabolomics

Glycomics is a relatively young scientific discipline that deals with structures and functions of natural carbohydrates. It evolves rapidly, and now we know that carbohydrates are important actors of various biological processes occurring both at…
GlyTorsion
Web

GlyTorsion

Allows to query the database GlyTorsionDB. GlyTorsion performs a graphical…

Allows to query the database GlyTorsionDB. GlyTorsion performs a graphical output of results by generating diagrams or plots. GlyTorsionDB contains the torsion angle values of all carbohydrate…

Carp
Web

Carp CArbohydrate Ramachandran Plot

Evaluates the quality of a protein 3D structure using protein backbone torsion…

Evaluates the quality of a protein 3D structure using protein backbone torsion angles. Carp permits users to query GlyTorsionDB, a database containing the torsion angle values of all carbohydrate…

GlycoMapsDB
Dataset

GlycoMapsDB

Provides a library compiling more than 2500 conformational maps of carbohydrate…

Provides a library compiling more than 2500 conformational maps of carbohydrate fragments originally described in the CARBBANK. GlycoMapsDB intends to help crystallographers to crosscheck their data…

Glyco 3D
Dataset

Glyco 3D

Offers a single entry to access threedimensional features of carbohydrate and…

Offers a single entry to access threedimensional features of carbohydrate and carbohydrate polymers. Glyco3D is a portal of databases covering the three-dimensional features of monosaccharides,…

GlyTouCan
Dataset

GlyTouCan

The international glycan structure repository. GlyTouCan is a freely available,…

The international glycan structure repository. GlyTouCan is a freely available, uncurated registry for glycan structures that assigns globally unique accession numbers to any glycan independent of…

CSDBs
Dataset

CSDBs Carbohydrate Structure Databases

Store structural, bibliographic, taxonomic, NMR spectroscopic, and other data…

Store structural, bibliographic, taxonomic, NMR spectroscopic, and other data on natural carbohydrates and their derivatives published in the scientific literature. The CSDB project was launched in…

GlycoRDF
Terminology

GlycoRDF

An ontology to define the RDF namespace, concepts and relationships between…

An ontology to define the RDF namespace, concepts and relationships between concepts to be used for exporting glycomics data into a standardized representation using RDF. The ontology contains…

doGlycans
Desktop

doGlycans

Allows users to prepare carbohydrate structures. doGlycans tool set is composed…

Allows users to prepare carbohydrate structures. doGlycans tool set is composed of two features: (i) prepreader.py, for preparing the carbohydrate chains for polymer simulations and; (ii)…

GMDB
Dataset

GMDB Glycan Mass Spectral DataBase

Provides a multistage tandem mass spectral (MS) database using a variety of…

Provides a multistage tandem mass spectral (MS) database using a variety of structurally defined glycans. GMDB offers a resource for glycomics research that enables users to identify glycans by…

Pdb2linucs
Web

Pdb2linucs

Generates a complete structural description of the complete glycan, which can…

Generates a complete structural description of the complete glycan, which can be easily transformed to the IUPAC nomenclature. Pdb2linucs is able to automatically extract carbohydrate information…

pdb-care
Web

pdb-care PDB CArbohydrate REsidue check

Identifies and assigns carbohydrate structures using only the reported atom…

Identifies and assigns carbohydrate structures using only the reported atom types and their 3D atom coordinates. pdb-care allows users to analyse a file obtained directly from PDB using the PDB-ID,…

GFDB
Dataset

GFDB Glycan Fragment Database

A database of the glycosidic torsion angles derived from the glycan structures…

A database of the glycosidic torsion angles derived from the glycan structures in the Protein Data Bank (PDB). The GFDB provides an intuitive glycan sequence search tool that allows the user to…

GAP
Web

GAP Glycome Analytics Platform

Offers the opportunity for open source development that integrates multiple web…

Offers the opportunity for open source development that integrates multiple web resources into reproducible workflows using Galaxy. The GAP’s integration of glycomics tools into an established…

GlycomeSeq
Web

GlycomeSeq

A computational approach to automate the sequencing of glycans using…

A computational approach to automate the sequencing of glycans using metadata-assisted glycan sequencing (MAGS), which combines mass spectrometry analyses with glycan structural information from…

UniCarbKB
Dataset

UniCarbKB

An initiative that aims to promote the creation of an online information…

An initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and…

GlycoSuiteDB
Dataset

GlycoSuiteDB

An annotated and curated relational database of glycan structures reported in…

An annotated and curated relational database of glycan structures reported in the literature. GlycoSuiteDB contains information on the glycan type, core type, linkages and anomeric configurations,…

GRITS Toolbox
Desktop

GRITS Toolbox

Enables high throughput comprehensive characterization of glycosylation where…

Enables high throughput comprehensive characterization of glycosylation where analysis of site of glycan attachment is important. GRITS Toolbox combines the analytical power of glycan permethylation…

GS-align
Desktop

GS-align

A computational method for glycan structure alignment and similarity…

A computational method for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and…

LINUCS
Desktop

LINUCS LInear Notation for Unique description of Carbohydrate Sequences

Converts the commonly used extended representation of complex carbohydrates…

Converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form. LINUCS can be applied on any molecules and to all types…

LfDB
Dataset

LfDB Lectin Frontier DataBase

Provides quantitative interaction data in terms of the affinity constants (Ka)…

Provides quantitative interaction data in terms of the affinity constants (Ka) of a series of lectins toward a panel of pyridylaminated (PA) glycans obtained by an automated frontal affinity…

GlycomeDB
Dataset

GlycomeDB

Integrates the structural and taxonomic data of all major public carbohydrate…

Integrates the structural and taxonomic data of all major public carbohydrate databases, as well as carbohydrates contained in the Protein Data Bank, which renders the database currently the most…

GlycoGAIT
Dataset

GlycoGAIT Glycosylation and Gut Associated Immune Tolerance

Identifies glycosylation relevance in gut barrier in response to commensal and…

Identifies glycosylation relevance in gut barrier in response to commensal and pathogenic bacteria for modulating the gut immune tolerance. The GlycoGAIT is a web database whose interface enables the…

Azahar
Desktop

Azahar

Extends the PyMOL's capabilities to visualize, analyze and model glycans…

Extends the PyMOL's capabilities to visualize, analyze and model glycans and glycoconjugated molecules. Azahar provides convenient functions to compute and visualize molecular properties useful…

GlycoMob
Dataset

GlycoMob

A freely accessible database containing over 900 collision cross section (CCS)…

A freely accessible database containing over 900 collision cross section (CCS) values of glycans, oligosaccharide standards and their fragments. GlycoMob is organized into three major sections…

GlycoNAVI
Dataset

GlycoNAVI

Provides access to carbohydrate research tools. GlycoNAVI is a database of…

Provides access to carbohydrate research tools. GlycoNAVI is a database of chemical reactions that involve carbohydrates and molecules involved in these reactions. The online interface of this…

GlyVicinity
Web

GlyVicinity

Allows statistical analyses on the types of amino acids around carbohydrate…

Allows statistical analyses on the types of amino acids around carbohydrate chains. GlyVicinity can also proceed analyses on atoms forming the closest contacts between protein and carbohydrate…

JCGGDB
Dataset

JCGGDB Japan Consortium for Glycobiology and Glycotechnology Database

A meta-database involving 15 original databases in AIST and 5 cooperative…

A meta-database involving 15 original databases in AIST and 5 cooperative databases in alliance with JCGG: Japan Consortium for Glycobiology and Glycotechnology. JCGGDB centers on a glycan structure…

GlycoCT
Format

GlycoCT

A format based on a connection table approach, instead of a linear encoding…

A format based on a connection table approach, instead of a linear encoding scheme, to describe the carbohydrate sequences, with a controlled vocabulary to name monosaccharides, adopting IUPAC rules…

Glyco-CD
Dataset

Glyco-CD

Provides a collection of lectins and carbohydrates. Glyco-CD offers information…

Provides a collection of lectins and carbohydrates. Glyco-CD offers information on 63 clusters of differentiation (CD) antigens. Lectins and carbohydrates are defined by CD antibodies that are…

GlycomeAtlas
Dataset

GlycomeAtlas

An innovative tool for analyzing glycan profiling data, without regard to the…

An innovative tool for analyzing glycan profiling data, without regard to the manner in which it has been obtained. GlycomeAtlas allows users to visualize and perform queries of glycome data.…

KEGG GLYCAN
Dataset

KEGG GLYCAN

Stores a collection of experimentally determined glycan structures. KEGG GLYCAN…

Stores a collection of experimentally determined glycan structures. KEGG GLYCAN is a publicly accessible database where a unique structure corresponds to an entry annotated with various information…

GLYCOSCIENCES.d…
Dataset

GLYCOSCIENCES.de

The development of glycan-related databases and bioinformatics applications is…

The development of glycan-related databases and bioinformatics applications is considerably lagging behind compared with the wealth of available data and software tools in genomics and proteomics.…

EUROCarbDB
Dataset

EUROCarbDB

Provides sophisticated, freely accessible, open-source informatics tools and…

Provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures,…

RINGS
Web

RINGS Ressource for Informatics of Glycomes at Soka

Provides algorithmic and data mining tools to aid glycobiology research. RINGS…

Provides algorithmic and data mining tools to aid glycobiology research. RINGS is a freely available Web resource for glycobiologists to analyze their data using the latest data mining and…

Lectindb
Dataset

Lectindb

Provides a knowledgebase for lectins. Lectindb is a manually curated database…

Provides a knowledgebase for lectins. Lectindb is a manually curated database which compiles sequences and structural information such as family classification or carbohydrate specificity for each…

PACDB
Dataset

PACDB Pathogen Adherence to Carbohydrate Database

Supplies information about pathogen adherence. PACDB is an online resource that…

Supplies information about pathogen adherence. PACDB is an online resource that offers users to find information by three ways: general search, search by diseases, or search by scientific names.

LiGraph
Web

LiGraph

Allows conversions of sugar graphs into ASCII IUPAC sugar nomenclature or as a…

Allows conversions of sugar graphs into ASCII IUPAC sugar nomenclature or as a graph.

GlycoEpitope
Dataset

GlycoEpitope

A large number of polyclonal or monoclonal antibodies have been used as very…

A large number of polyclonal or monoclonal antibodies have been used as very important tools for analyzing expression of various carbohydrate chains and their functions. In this database, useful…

GlycoPOD
Dataset

GlycoPOD GlycoScience Protocol Online Database

Aims to fill the gaps between the beginners and experts by delivering the…

Aims to fill the gaps between the beginners and experts by delivering the accumulated knowledge and skills of the experts to the beginners through internet communication under the catch-phrase of…

GGDB
Dataset

GGDB GlycoGene Database

Stores information on substrate specificity. GGDB provides necessary…

Stores information on substrate specificity. GGDB provides necessary information for the analysis of glycogenes. In GGDB, the following property information of each glycogene are stored in XML…

CSS
Dataset

CSS Carbohydrate Structure Suite

Compiles carbohydrate structures from the Protein Data Bank (PDB) in a…

Compiles carbohydrate structures from the Protein Data Bank (PDB) in a standardized way. CSS intends to detect and assign carbohydrate 3D structures, analyzes them and provides the results. The…

GDB:Structures
Dataset

GDB:Structures Glycoconjugate Data Bank:Structures

Provides access to annotated glycan structures. GDB:Structures is a database…

Provides access to annotated glycan structures. GDB:Structures is a database that contains glycans classified into three types: ligands, N-glycans and O-glycans. Users can retrieve lists of glycans…

AnimalLectinDb
Dataset

AnimalLectinDb

Compiles data about animals’ lectins. AnimalLectinDb is a manually curated…

Compiles data about animals’ lectins. AnimalLectinDb is a manually curated database with aim of collecting an exhaustive information about this carbohydrate-binding protein class including Express…

GlycomicsDB
Dataset

GlycomicsDB

Incorporates mass spectrometry experiment data from disparate sources. Then, it…

Incorporates mass spectrometry experiment data from disparate sources. Then, it can organize them into a uniformed format for users to share. GlycomicsDB offers the possibility for collaborating…

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