Comparative β-Propeller Alignments

<p>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) [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0040010#pcbi-0040010-b043" target="_blank">43</a>].</p

Comparative β-Helix Alignments

<p>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) [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0040010#pcbi-0040010-b043" target="_blank">43</a>].</p

Distinguishing Alignable Structures from Decoys

<p>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.</p

Matt SABmark Performance Tradeoffs

<p>Average pairwise RMSD versus average number of residue positions placed in the common core for the SABmark superfamily benchmark.</p

Overview of the Matt Algorithm

<p>Overview of the Matt Algorithm</p

Two Sequential Block Pairs that Could Form Part of an Assembly

<p>Block pair <i>BC</i> precedes block pair <i>DE</i> because <i>B</i> precedes <i>D</i> and <i>C</i> precedes <i>E</i> in their respective protein sequences.</p