Fig. 2: Schematic overview of GAP used to build the GlycoShape GDB.

a, Multiple uncorrelated replica MD simulations are performed for each glycan in the GDB, to comprehensively sample its structural dynamics. b,c, The resulting MD frames are then transformed into a graph matrix representation (b), simplified by flattening the lower half as a mono-dimensional array (c). d, This step enables a dimensionality reduction via PCA. e, These data are clustered by GMM, the results of which are displayed in terms of cluster distributions. f, Representative 3D structures for each cluster are selected on the basis of KDE maxima, along with comprehensive torsion angle profiles for the highest-populated clusters, showing the wide breadth of the conformational space covered by GAP. g, Structures derived from GAP are clearly presented on the GlycoShape GDB web platform, in addition to biological and chemical information.