David F. Thieker, Jodi A. Hadden, Klaus Schulten, and Robert J. Woods.
3D implementation of the symbol nomenclature for graphical
representation of glycans.
Glycobiology, 26:786-787, 2016.
(PMC: PMC5018049)
THIE2016
The representation of protein 3D structures in the now-ubiquitous ribbon format profoundly aids in simplifying the visualization of protein structures, enabling rapid recognition of similarities and differences between protein domains. While ribbon representations can also be convenient for illustrating the 3D features of regular repeating polysaccharide structures, the lack of highly ordered structural motifs in most oligosaccharides (glycans) attenuates the information content of such representations. The widely accepted 2D glycan symbol nomenclature developed in the 2nd edition of the Essentials of Glycobiology textbook, quickly communicates glycan sequence according to a system of shapes and colors for monosaccharides, and has recently been expanded and renamed the Symbol Nomenclature for Glycans (SNFG). However, it does not convey an appreciation for the 3D structure of the glycans. Attempts to incorporate early versions of such symbols into glycan 3D structures have been proposed, but to date the most common representations remain formats in which the atoms of the glycan are simply colored according to the SNFG scheme. In an effort to popularize and simplify the visualization of 3D glycan structures, we present here a 3D adaptation of the new SNFG nomenclature, which we term the 3D Symbol Nomenclature for Glycans (3D-SNFG), and have implemented it for use with the visual molecular dynamics (VMD) program.
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