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Updated: Sep 30, 2025

Hierarchical and Programmable One-Pot Oligosaccharide Synthesis
Published on: September 6, 2019
Carbohydrate Structure Database oligosaccharide conformation tool
Sofya I Scherbinina1, Martin Frank2, Philip V Toukach3
1Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya square 9, Moscow 125047, Russia.
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.
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