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. Author manuscript; available in PMC: 2022 Apr 1.
Published in final edited form as: Structure. 2021 Mar 2;29(4):393–400.e1. doi: 10.1016/j.str.2021.02.004

Table 1.

Summary of wwPDB Validation Software Integration SNFG: standard monosaccharide Symbol Nomenclature For Glycans

Feature Details Software Package(s)
Atomic coordinates and bond order information for all ligands Extracts LOI (Ligand Of Interest) ligands and WURCS descriptor of branched entities for carbohydrates from the atomic coordinate file Maxit (Feng) PDB2Glycan (gitlab.com/glyconavi/pdb2glycan)
2D SNFG images Generates 2D SNFG images using wurcs2pic software that uses GlycanBuilder2 as a library, if WURCS descriptors are present in the branched entities wurcs2Pic (gitlab.com/glycoinfo/wurcs2pic) GlycanBuilder2 (Tsuchiya, et al., 2017)
Geometric quality assessment Mogul is used to assess geometric quality for all ligands. Mogul (Bruno, et al., 2004)
2D image of quality Creates 2D graphical depiction of Mogul quality analyses for each LOI and/or each branched oligosaccharide buster-report (SmartBricogne, 2015)
3D graphical views Creates 3D graphical views of electron density difference maps for each LOI and/or each branched oligosaccharide buster-report (SmartBricogne, 2015)