Figure 1.
Scheme of the FragIt Algorithm.
Figure 2.
Pattern matching on a peptide bond using SMARTS.
Table 1.
Patterns of Fragmentation.
Figure 3.
Protein Backbone Fragmentation Example.
An example of how fragmentation and protection is carried out using SMARTS patterns on a protein in FragIt. Illustration a) is the uncorrupted protein backbone with side-chains R1 through R4, b) shows how a protection pattern matches atoms very specifically. c) and d) shows examples of fragmentation using the standard peptide pattern supplied in this work. Finally, e) is the final fragmentation when all fragmentation (4 fragments) and protection (1 fragment) is carried out, resulting in 3 fragments.
Table 2.
Default Fragmentation Results.
Figure 4.
Different fragmentation options illustrated for Chignolin.
Here shown a) without protection and no grouping, b) with protection and no grouping, c) without protection but in groups of two residues per fragment and d) with protection and using two residues per fragment. We use a six color coloring scheme resulting in different fragments may have the same color.
Table 3.
Fragmentation of Chignolin using various options for FragIt and FMOutil.
Figure 5.
An example of how fragmentation is carried using SMARTS patterns on a polysaccharide molecule in FragIt. Illustration a) is the polysaccharide molecule of interest, in this case an D-galactopyranose trimer. b) and c) shows examples of fragmentation using the polysaccharide fragmentation pattern in this work. Finally, d) shows the final fragmentation of 3 fragments.
Figure 6.
Fragmentation of DNA using FragIt.
We use a six color coloring scheme resulting in different fragments may have the same color.
Figure 7.
Fragmentation of Leucoemeraldine (a Polyaniline) using FragIt.
This particular example uses no fragmentation patterns but rather explicitly defined points of fragmentation by the end user.
Figure 8.
Different active, inactive and frozen regions in Chignolin.
Regions are color-coded according to their function: red is active, blue is buffer and green is frozen. In a) fragment 1 is in the active region, fragments 2, 3, 6–9 are buffer region fragments and fragments 4 and 5 are in the frozen region. In b), fragments 1,2,6 and 8 are active fragments while fragments 3,4,5,7 and 9 are buffer region fragments. There are is no frozen region in b).
Figure 9.
Fragmentation of Chignolin using the web service.