Carbohydrate Structure Database oligosaccharide conformation tool. (10th March 2022)

• Record Type: Journal Article
• Authors: Scherbinina, Sofya I; Frank, Martin; Toukach, Philip V
• Is Part Of: Glycobiology. Volume 32:Number 6(2022)
• Page Start: 460
• Page End: 468
• Publication Date: 2022-03-10
• Subjects: conformational map -- CSDB -- database -- glycosidic linkage -- molecular dynamics; Glycoproteins -- Periodicals; Glycolipids -- Periodicals; Glycoconjugates -- Periodicals; 572.567
• DOI: 10.1093/glycob/cwac011
• Languages: English
• ISSNs: 0959-6658

Abstract

Abstract: Population analysis in terms of glycosidic torsion angles is frequently used to reveal preferred conformers of glycans. However, due to high structural diversity and flexibility of carbohydrates, conformational characterization of complex glycans can be a challenging task. Herein, we present a conformation module of oligosaccharide fragments occurring in natural glycan structures developed on the platform of the Carbohydrate Structure Database. Currently, this module deposits free energy surface and conformer abundance maps plotted as a function of glycosidic torsions for 194 "inter"residue bonds. Data are automatically and continuously derived from explicit-solvent molecular dynamics (MD) simulations. The module was also supplemented with high-temperature MD data of saccharides (2, 403 maps) provided by GlycoMapsDB (hosted by GLYCOSCIENCES.de project). Conformational data defined by up to 4 torsional degrees of freedom can be freely explored using a web interface of the module available at http://csdb.glycoscience.ru/database/core/search_conf.html . Graphical Abstract: