3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans
In an effort to popularize and simplify the visualization of 3D glycan structures, we present here a 3D adaptation of the new SNFG nomenclature (Varki 2015), which we term the 3D Symbol Nomenclature for Glycans (3D-SNFG), and have implemented it for use with the Visual Molecular Dynamics (VMD) program. VMD was selected as an initial platform because it is widely used for visualizing molecular structures, as well as data from molecular dynamics simulations.
This concept has also been expanded here to create a hybrid atomistic-symbolic representation, in which proportionally-reduced 3D-SNFG symbols (3D-SNFG Icons) are placed on the centroids of the monosaccharide rings. By providing simultaneous communication of glycan sequence and atomic interactions, the 3D-SNFG icon mode enables rapid monosaccharide recognition while maintaining structural detail.