Table 1.
Homstrad Performance Comparison
Table 2.
SABmark Superfamily Performance Comparison
Table 3.
SABmark Twilight Zone Performance Comparison
Figure 1.
Overview of the Matt Algorithm
Figure 2.
Matt Homstrad Performance Tradeoffs
Average pairwise RMSD versus average number of residue positions placed in the common core for the Homstrad multiple alignment benchmark.
Figure 3.
Matt SABmark Performance Tradeoffs
Average pairwise RMSD versus average number of residue positions placed in the common core for the SABmark superfamily benchmark.
Figure 4.
Comparative β-Propeller Alignments
The four SABmark domains in the set Group 137, consisting of seven-bladed β-propellers as aligned by Posa, Mustang, MultiProt, and Matt. Backbone atoms that participate in the common core of the alignment show up colored as red (PDB ID d1nr0a1), green (PDB ID d1nr0a2), blue (PDB ID d1p22a2), and magenta (PDB ID d1tbga); residues in all four chains that are not placed into the alignment by the tested algorithm are shown in gray. These pictures were generated by the Swiss PDB Viewer (DeepView) [43].
Figure 5.
Comparative β-Helix Alignments
Aligned portions of the eight SABmark domains in the set Group 144, consisting of the left-handed β-helix fold as aligned by Posa, Mustang, MultiProt, and Matt. Backbone atoms that participate in the common core of the alignment show up colored as red (PDB ID d1hm9a1), green (PDB ID d1kk6a), blue (PDB ID d1krra), magenta (PDB ID d1lxa), yellow (PDB Is that are not placed into the alignment by the tested algorithm are shown in gray. These pictureD d1ocxa), orange (PDB ID d1qrea), cyan (PDB ID d1xat), and pink (PDB ID d3tdt); residues in all three chains were generated by the Swiss PDB Viewer (DeepView) [43].
Table 4.
Example of Multiple Structure Alignments in the Two Figures from the SABmark Benchmark Dataset
Figure 6.
Distinguishing Alignable Structures from Decoys
Positive (blue) and SABmark decoy (red) pairwise alignments plotted by RMSD versus number of residues for Matt, FlexProt, MultiProt, and Mustang on the SABmark superfamily set.
Table 5.
Discrimination Performance on the SABmark Superfamily Set
Table 6.
Discrimination Performance on the SABmark Twilight Zone Set
Figure 7.
Two Sequential Block Pairs that Could Form Part of an Assembly
Block pair BC precedes block pair DE because B precedes D and C precedes E in their respective protein sequences.