Building oligosaccharides with YASARA

YASARA Dynamics and YASARA Structure provide an interactive oligosaccharide builder, with on-the-fly energy minimization:

- Click Edit > Build > Oligosaccharide.
- Select the first monosaccharide to start with, choosing between alpha/beta and D/L-isomers (Figure 1).
- Select the next monosaccharide to join (marking the two hydroxyl groups that should form the glycosidic bond) and watch YASARA perform the oligomerization, derive force field parameters and energy minimize the growing oligosaccharide (Figure 2). The example movie shows how lactose is built from galactose and glucose.
- Continue joining additional building blocks or add other modifications.