CARBOHYDRATE STRUCTURE DATABASE OLIGOSACCHARIDE CONFORMATION TOOL
1Higher Chemical College, Mendeleev University of Chemical Technology of Russia, Moscow, Russia
2Biognos AB, Göteborg, Sweden
3N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
KEYWORDS: CSDB, glycosidic linkage, conformational map, database, molecular dynamics
Glycobiology, 2022, v.32(6), pp. 460-468
DOI: 10.1093/glycob/cwac011, PMID: 35275211
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 (CSDB). 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 (2403 maps) provided by GlycoMapsDB (hosted by GLYCOSCIENCES.de project). Conformational data defined by up to four 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.
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