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Article

GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans

1
University Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
2
SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
3
Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
4
Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland
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Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS—Université Lyon 1, 69622 Villeurbanne CEDEX, France
6
Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia
*
Author to whom correspondence should be addressed.
Biomolecules 2020, 10(12), 1660; https://doi.org/10.3390/biom10121660
Received: 20 November 2020 / Revised: 3 December 2020 / Accepted: 9 December 2020 / Published: 11 December 2020
Glycosaminoglycans (GAGs) are complex linear polysaccharides. GAG-DB is a curated database that classifies the three-dimensional features of the six mammalian GAGs (chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate) and their oligosaccharides complexed with proteins. The entries are structures of GAG and GAG-protein complexes determined by X-ray single-crystal diffraction methods, X-ray fiber diffractometry, solution NMR spectroscopy, and scattering data often associated with molecular modeling. We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. Special attention was devoted to the description of the bound glycan ligands using simple graphical representation and numerical format for cross-referencing to other databases in glycoscience and functional data. GAG-DB provides detailed information on GAGs, their bound protein ligands, and features their interactions using several open access applications. Binding covers interactions between monosaccharides and protein monosaccharide units and the evaluation of quaternary structure. GAG-DB is freely available. View Full-Text
Keywords: glycosaminoglycans; three-dimensional structure; database; polysaccharide conformation; protein-carbohydrate interactions glycosaminoglycans; three-dimensional structure; database; polysaccharide conformation; protein-carbohydrate interactions
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MDPI and ACS Style

Pérez, S.; Bonnardel, F.; Lisacek, F.; Imberty, A.; Ricard Blum, S.; Makshakova, O. GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. Biomolecules 2020, 10, 1660. https://doi.org/10.3390/biom10121660

AMA Style

Pérez S, Bonnardel F, Lisacek F, Imberty A, Ricard Blum S, Makshakova O. GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. Biomolecules. 2020; 10(12):1660. https://doi.org/10.3390/biom10121660

Chicago/Turabian Style

Pérez, Serge, François Bonnardel, Frédérique Lisacek, Anne Imberty, Sylvie Ricard Blum, and Olga Makshakova. 2020. "GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans" Biomolecules 10, no. 12: 1660. https://doi.org/10.3390/biom10121660

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