Prof. Vered Padler-Karavani Lab

Below we are forwarding you to the most comprehensive websites for Glycorelated research.

 

​Essentials of Glycobiology textbook, 4th edition

Editors: Ajit Varki, Richard D. Cummings, Jeffrey D. Esko, Pamela Stanley, Gerald W. Hart, Markus Aebi, Debra Mohnen, Taroh Kinoshita, Nicolle H. Packer, James H. Prestegard, Ronald L. Schnaar, and Peter H. Seeberger. Cold Spring Harbor (NY): 2022.

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The Human Glycom Project (HPG) 

(HGP) is a consortium of research groups that shares a common goal to define the structures and functions of human glycoconjugates. The HPG projects and Database are listed.

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Functional Glycomics Gateway

The Functional Glycomics Gateway is a comprehensive resource for functional glycomics research brought to you by the Consortium for Functional Glycomics (CFG).

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National Center for Functional Glycomics (NCFG) 

The National Center for Functional Glycomics (NCFG) at Emory University School of Medicine, is one of four Glycomics-related Biomedical Technology Resource Centers (BTRC) in the U.S., funded by the National Institutes of Health. Analogous to Genomics and Proteomics, Glycomics focuses on defining the structures and functions of complex carbohydrates, as found in glycoproteins, glycolipids, and glycosaminoglycans. The specific focus of the NCFG is on technology development in the glycosciences with an emphasis on exploring the molecular mechanisms of glycan recognition by proteins important in human biology and disease. 

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GlyCosmos portal

Integration of diverse omics data including glycogenes, glycoconjugates (such as glycoproteins and glycolipids), molecular structures, and pathways. This portal site  include the development of a new glycoconjugate repository GlyComb, as well as an integrated and curated database under GlyCosmos which provides context for the glycans and glycoconjugates registered in the GlyTouCan and GlyComb repositories, respectively. In addition, this project involve development of standard notations (WURCS) and ontologies (GlycoRDF, Glycoconjugate ontology). By using Sematic Web technologies, GlyCosmos  also integrate other -omics databases from the fields of genomics, proteomics, metabolomics and lipidomics.

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GlyGen 

GlyGen is a computational and informatics resources for Glycoscience data. It is an integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. This web portal allows exploring this data and performing unique searches that cannot be executed in any of the integrated databases alone.

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Glyco@Expasy 

Expasy portal that facilitate the use of bioinformatics in glycoscience and the relation between glycobiology and protein-oriented bioinformatics resources. It is gradually populated with web-based resources developed in-house as well as externally.

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GlySpace Alliance

Integration of the 3 bioinformatic portals (GlyCosmos, GlyGen and GlycoExpasy) for collaborative global glycoinformatics community.

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European Glycoscience Community 

The EGC is a pan-European Glycoscience network that identify and solve scientific challenges through cross-sectorial collaborative engagement, ensure EU funding opportunities, engage with industry to translate fundamental science to products and services, and establish national Glycoscience research networks to for Europe wide initiatives that support Glycoscience R&D. For this purpose, the EGC map highlights expertise across Europe where each pin show centers of expertise, facilities, suppliers and capabilities and how to access them.

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Glycobiology centers 

• Congenital Disorders of Glycosylation, Children’s Hospital of Philadelphia

• Complex Carbohydrate Research Center, University of Georgia (UGA)

• National Center for Glycomics and Glycoproteomic, Indiana University Bloomington

• Glycobiology Research and Training Center, UC San Diego (UCSD)

• Harvard Medical School Center for Glycoscience

• Society for Glycobiology

• Gordon Research Conference on Glycobiology

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Carbohydrate structures databases

• KEGG Glycan database - collection of glycan structures

• Glycosciences.de - 3D structures, 3D structure models and references to PDB entries

• PDB2-LINUCS Glycoproteins in PDB

• dbPTM: Structural database for protein post-translational modification

• CFG- Glycan Structures Database 

• Bacterial Carbohydrate Structure DataBase

• CarbBank

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Glycan building and drawing

• Glycan Builder

• GLYCO3D

• LINUCS Linear encoding of sugars

• CabosML Carbohydrate sequence markup Language

• KegDraw

• LiGraph Graphical representation

• Expasy Glycan Mass

• GLYCAM Generation of 3D structures

 

Glycan synthesis and  pathways 

• GGDB human glycogenes

• KEGG orthology glycosyltransferases

• KEGG pathway carbohydrate metabolism

• CAZy carbohydrate active enzymes

• SphinGOMAP pathways of sphingolipid biosynthesis

 

Glycan Binding Proteins

• Database of Anti-Glycan Reagents (DAGR)

• Genomics Resource for Animal Lectins

• UniLectin3D- 3D structure of lectins

• CFG Glycan Binding Proteins

• CFG Microarray Data

• GlycoEpitope- encyclopedia of carbohydrate antigens- glyco-epitopes and antibodies

• LectinDB: Lectin Database

• SugarBindDB: Bacterial lectin Database and carbohydrate sequences pathogenic organisms (bacteria, toxins and viruses) specifically adhere.

 

Prediction of glycosylation sites

• Isoform Specific O-Glycosylation Prediction (ISOGlyP)

• N-glycosylation sites predicting- NetNGlyc

• O-glycosylation sites predicting- NetOGlyc

• O-ß-GlcNAc and phosphorylation prediction- YinOYang

• GPI-anchor prediction- big-PI Predictor

• Expasy GlycoMod- Predict possible oligosaccharide structures from their experimentally determined masses.

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Nomenclature​

• CFG Nomenclature

• IUPAC Nomenclature

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General links

• NIH 

• Current Protocols issues      

• Pubmed​

• PDB - repository DB of all 3D bio-structures