☆ 4.7 Article

Rapidly Display Glycan Symbols in 3D Structures: 3D-SNFG in LiteMol

JOURNAL OF PROTEOME RESEARCH (2019)

Journal

JOURNAL OF PROTEOME RESEARCH

Volume 18, Issue 2, Pages 770-774

Publisher

AMER CHEMICAL SOC

DOI: 10.1021/acs.jproteome.8b00473

Keywords

oligosaccharide; glycan; carbohydrate; glycoprotein; SNFG; 3D-SNFG; visualization; LiteMol; structure; symbol nomenclature for glycans

Categories

Biochemical Research Methods

Funding

National Institutes of Health [U01CA207824]
ELIXIR-EXCELERATE project [676559]
ELIXIR CZ research infrastructure project [LM2015047]
European Regional Development Fund-Project ELIXIR-CZ [CZ.02.1.01/0.0/0.0/16_013/0001777]
Wellcome Trust [104948]
EMBL-EBI funding

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Abstract

The representation of carbohydrates in 3D space using symbols is a powerful visualization method, but such representations are lacking in currently available visualization software. The work presented here allows researchers to display carbohydrate 3D structures as 3D-SNFG symbols using LiteMol from a web browser (e.g., v.litemol.org/?loadFromCS=5T3X). Any PDB ID can be substituted at the end of the URL. Alternatively, the user may enter a PDB ID or upload a structure. LiteMol is available at https://v.litemol.org and automatically depicts any carbohydrate residues as 3D-SNFG symbols. To embed LiteMol in a webpage, visit https://github.com/dsehnal/LiteMol.

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