Databases

Other specialized Databases

Protein Data Bank is a single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. Also see, Human Protein Atlas, a Sweden-based program that aims to map all the human proteins in cells, tissues, and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology.
Additionally, AlphaFold server provides a database of 3D structures of all known proteins predicted by the AlphaFold 3, a powerful AI-based software for which the developers won Nobel Prize in chemstry in 2024, READ MORE. Also, see PATHpre for predictive modeling of protein dynamics.
EuPathDB is a portal providing access to the resources for research on Eukaryotic pathogens. Read here for More
GlySpace Alliance consists of three major glycan-related database integration projects: GlyGen, Glyco@Expasy and GlyCosmos (see these under Portals).
The Cancer Genome Atlas (TCGA) provides a rich dataset that enhances our understanding of cancer biology and informs the development of targeted therapies. Also see, glycan data (OncoDB.Glycogene) related to TCGA.

GlycobioInformatics Databases

List of some selected databases that are often used for glycobioinformatics analysis. (see: Publication, chapter 16 (page 323-375), for a short description)

CAZy

Carbohydrate Active EnZyme database. More information is available in the cazy Web site.

GlycoGeneDB (GGDB)

Glyco enzyme database. More information is available in the website.

GlycoEpitope

On Glycan Binding Proteins. Also available at GlyCosmos.

GlyTouCan

An International glycan structure repository. See this Publication.

JCGGDB

Querying among multiple Japanese databases (also see, ACGG Databases)

A Database of glycans, glycosyltransferases, glycosidases, and related, a module of this portal (GW). This is designed as a dynamic web resource that would provide continually updated expert-driven descriptions of every glycan molecules and related entities.

PolySac3DB

A Database of Polysaccharide 3D structures.

UniLectin3D

A Database of Lectin 3D structures providing a knowledge base of curated and predicted lectins.

UniProt

A protein database with notation on glycosylation site/s. See the Publication here and also here

for its application in mass spectrometry-based proteomics.

Other Useful Databases

CSDB provides several tools for statistical analysis of bacterial, plant and fungal glycomes. For description, see here.

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