YASARA provides 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
Figure 1: Building oligosaccharides,
choosing the first monosaccharide
Figure 2: Screen
recording of YASARA's interactive oligosaccharide builder, showing how
lactose is built from
galactose and glucose. A higher quality version
can be watched at YouTube,
click on 'Watch in high quality' below the video.