Fig. 3: Schematic overview of the Re-Glyco algorithm used to select and link glycan 3D structures from the GDB to a protein.

a, The definition of the φ and ψ torsion angles, with corresponding atoms labeled ‘a’ to ‘e’, determining the conformation of the linkage between the protein (P shown in gray) sidechain and the reducing end of the glycan (G shown in yellow). b, Heat maps showing preferential conformation of the φ, ψ torsions between Asn-b-GlcNAc and Thr-a-GalNAc, with energy minima highlighted within red rectangles. c, Two-dimensional SNFG structure and (below) 3D structures of the tetra-antennary fully a3-sialylated N-glycan from the clustering analysis shown in Fig. 1. d, A schematic representation of the Re-Glyco workflow applied to the reconstruction of human interleukin-5 (IL5; Uniprot P05113). In agreement with the annotation⁸⁴, GlcNAc Scanning identifies only the N47 sequon as potentially occupied. Accordingly, N47 can be functionalized with more elaborate structures through a ‘one-shot’ glycosylation, where also T22 can be functionalized with a sialylated core1 O-glycan. Highly complex glycosylation at N47 and alternative O-glycosylation structures can be selected by sourcing directly from the GDB through the Advanced (Site-by-Site) Glycosylation tool, as shown on the alternative IL5 glycoform on the righthand side. Molecular rendering with Mol* Viewer⁸⁵; statistical analysis and heat maps created with matplotlib (https://matplotlib.org/).