BETASCAN output for amyloid and prion proteins with experimentally determined β-structures. W. Bryan Jr.Allen MenkeMatthew J. CowenLenore L. LindquistSusan BergerBonnie 2009 <p>Green vertical brackets indicate experimentally derived locations of β-strands; blue brackets indicate locations determined by a separate method. In the same manner as <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi-1000333-g001" target="_blank">Figure 1b</a>, BETASCAN predictions are marked as horizontal lines, shading from red (maximum predicted score) to yellow (zero score, i.e., probability equal to background). Overlapping lines indicate alternate folding patterns for the β-strands, with indicated probability. Two graphs are included to display the results for each orientation of the strand. For purposes of comparison, the set of highest-scoring non-overlapping strands in the BETASCAN single-strand prediction was taken as the predicted structure. Corresponding outputs of PASTA <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-Trovato1" target="_blank">[49]</a>,<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-Trovato2" target="_blank">[50]</a>, TANGO <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-FernandezEscamilla1" target="_blank">[45]</a>, and Zyggregator <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-Tartaglia1" target="_blank">[46]</a> are displayed below the BETASCAN results. Refer to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi-1000333-t001" target="_blank">Table 1</a> for a summary of the correspondences of these predictions. (A) amyloid-β structure as determined by Luehrs et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-Petkova1" target="_blank">[18]</a> (green) and Petkova et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-Luhrs1" target="_blank">[19]</a> (blue); (B) het-S structure as determined by Ritter et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-Ritter1" target="_blank">[20]</a> (green) and Wasmer et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-Wasmer1" target="_blank">[21]</a> (blue); (C) α-synuclein structure as determined by Heise et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-Heise1" target="_blank">[51]</a>; (D) amylin structure as determined by Kajava et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-Kajava2" target="_blank">[53]</a>; (E) tau protein fragment PHF43 structure as determined by von Bargen et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000333#pcbi.1000333-vonBergen1" target="_blank">[52]</a>.</p>