Fig. 1. The 3DCOMB algorithm overview.

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Fig. 1. The 3DCOMB algorithm overview. From: Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling Bioinformatics. 2011;27(18):2537-2545. doi:10.1093/bioinformatics/btr432 Bioinformatics | © The Author 2011. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Fig. 2. MSA upper bound analysis on three datasets (a) HOMSTRAD, (b) SABmark-sup and (c) SABmark-twi. The X-axis is of the MSAs generated by 3DCOMB and the Y-axis is the estimated difference between the 3DCOMB alignments and the best possible. From: Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling Bioinformatics. 2011;27(18):2537-2545. doi:10.1093/bioinformatics/btr432 Bioinformatics | © The Author 2011. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Fig. 3. The pictures in (a1), (b1) and (c1) show the 3DCOMB alignments of SABmark-sup 323, SABmark-twi 124 and SABmark-twi 118, respectively. Proteins are displayed in different colors. The full-core positions (where all proteins are aligned) are displayed in ribbon while the partial-core positions (where >50% of proteins are aligned) in strand. The pictures in (a2), (b2) and (c2) show the ligand positions of the three structure groups (in spacefill form) and ConCavity predictions with confidence in colors. Color close to blue indicates low confidence while close to red high, while gray indicates no predictions at all. (a1) The proteins in blue, green and red are d1qh4a2, d1m15a2 and d1f52a2, respectively. (a2) The ligand ADP is from 1m15. (b1) The proteins in blue, cyan, dark green, light green, yellow and red are d1lw9a_, d1qgia_, d153l__, d1dxja_, d3lzt__ and d1qsaa2, respectively. (b2) The ligand GlcN6 is from 1qgi. (c1) The proteins in blue, cyan, dark green, light green, yellow and red are d1qgoa_, d1doza_, d1toaa_, d1n2za_, d1m1na_ and d1m1nb_, respectively. (c2) The ligand heme is from 1doz. From: Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling Bioinformatics. 2011;27(18):2537-2545. doi:10.1093/bioinformatics/btr432 Bioinformatics | © The Author 2011. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com