CSDB/SNFG STRUCTURE EDITOR: AN ONLINE GLYCAN BUILDER WITH 2D AND 3D STRUCTURE VISUALIZATION
1 N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
2 Faculty of Chemistry, National Research University Higher School of Economics, Moscow, Russia
KEYWORDS: online glycan builder, carbohydrate molecule editor, 3D structure, atomistic format, GlycoCT, CSDB, SNFG, API, online
Journal of Chemical Information and Modeling, 2021, v.61(10), pp. 4940-4948
DOI: 10.1021/acs.jcim.1c00917, PMID: 34595926
This article describes features, usage, and application of an CSDB/SNFG Structure Editor, a new online tool for quick and intuitive input of carbohydrate and derivative structures using Symbol Nomenclature for Glycans (SNFG). The Editor is built on a platform of the Carbohydrate Structure Database (CSDB) and relies on its online services via the dedicated web-API. The Editor allows building of oligo- and polymeric glycan structures and supports most features of natural glycans, such as underdetermined structures, alternative branches, repeating subunits, SMILES specification of atypical monomers, and others. The vocabulary of building blocks contains 600+ monomeric residues, including 327 monosaccharides. Support for SMILES allows input and visualization of chemical structures of virtually unlimited complexity. On the other hand, the interface follows the recognized GlycanBuilder style easy to novice users. The export feature includes support for CSDB Linear, GlycoCT, WURCS, SweetDB, and Glycam notations, SMILES codes, MOL/PDB atomic coordinate formats, raster and vector SNFG images, and on-the-fly visualization as 2D structural formulas and 3D molecular models. Integration of the Editor into any web-based glycoinformatics project is straightforward and simple, similarly to any other modern JavaScript application.
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