BIOINFORMATICS Vol. 00 no. 00 2012Pages 1–10

Fast Protein Structure Alignment using Gaussian OverlapScoring of Backbone Peptide Fragment SimilarityDavid W. Ritchie1∗, Anisah W. Ghoorah1,2, Lazaros Mavridis3, and VishweshVenkatraman4

1Inria Nancy, 615 Rue du Jardin Botanique, 54600 Villers-les-Nancy, France2Universite de Lorraine, LORIA, 54506 Nancy, France3University of St. Andrews, St. Andrews KY16 9AJ, Scotland, UK4Norwegian University of Science and Technology, Høgskoleringen 5, Trondheim, Norway

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∗to whom correspondence should be addressed

c© Oxford University Press 2012. 1

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Supplementary Figure 1. (continued)

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Protein Structure Alignment

Supplementary Figure 1. Cartoon representations of the secondary structure assigments calculated by Stride, DSSP, and Kpax for ten example structuresselected from the ten pairs of structures from Fischeret al. (1996). Secondary structure elements are coloured according toα-helix: blue; 3-10-helix: mauve;β-strand: green; turn: yellow; loop/coil: red. By construction, Kpax detects only helices and strands, and it calls all other regions as loop/coil.

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Supplementary Figure 2. (continued)

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Protein Structure Alignment

Supplementary Figure 2. Cartoon representations of the superpositions calculatedby CE, Sheba, TM-Align, and Kpax for the ten alignment examples ofFischeret al. (1996) drawn in the same order as Table 1 (see Table 1 for RMSDs). In each image, the fixed (reference) structure is shown with all α-helicesandβ-strands drawn in red. The superposed structures are shown with α-helices in blue andβ-strands in green. For all structures, 3-10 helices are shownin mauve, and turns are shown in yellow. For each row, the close correspondence of the positions of the blueα-helices and greenβ-strands shows that eachalignment algorithm is correctly recognising and superposing each pair of protein folds. All images are drawn using Stride SSE assignments.

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Supplementary Table 1. The RMSDs between the calculated positions of the moving structure with respect to a fixed reference structure for each ofthe tenpairs of structures from Fischeret al. (1996) when superposed by CE, Sheba, TM-align, and Kpax.∗

CE Sheba TM-AlignSheba Kpax TM-Align Kpax CE Kpax

1fxiA/1ubqA 2.46 4.76 2.83 4.57 1.78 3.831tenA/3hhrB 0.59 0.72 0.37 0.27 0.89 0.373hlaA/2rheA 2.46 3.96 5.94 6.30 3.62 1.112azaA/1pazA 4.03 0.84 1.65 3.55 2.90 2.581cewI/1molA 2.07 1.49 0.57 1.31 1.70 0.921cidA/2rheA 1.93 1.15 0.49 1.00 1.55 0.751crlA/1edeA 3.53 1.71 2.88 3.48 1.80 1.002simA/1nsbB 1.08 0.82 0.70 0.90 0.60 0.421bgeB/2gmfA 8.34 5.44 4.59 4.95 4.69 1.721tieA/4fgfA 1.21 1.24 0.17 0.69 1.01 0.38

Average 2.77 2.21 2.04 2.70 2.05 1.31

∗This table lists theCα RMSD (A units) between the coordinates of the moving structure when calculated by a specific pair of structuralalignment methods with respect to a fixed reference structure. For example, the first element of the first row shows that theCα RMSDbetween the superposed positions of ubiquitin (chain A of PDB code 1ubq) when calculated by CE and Sheba is 2.46A. The final row ofthe table shows the average RMSD between the coordinates of the moving structures as calculated by each pair of alignmentmethods. Forexample, the last element of the final row shows that the average RMSD between the superpositions of TM-Align and Kpax is 1.31A, whichis less than that of all other pairs of alignment methods. In other words, on average, the Kpax alignments are more similarto the TM-Alignalignments than the alignments calculated by either CE or Sheba.

Supplementary Figure 3. Close-up view of the structural alignments calculated by TM-Align and Kpax for the pair 1fxiA/1ubqA (ferrodoxin/ubiquitin). Ineach image, theα-helices andβ-strands of the fixed reference structure (here, ferrodoxin) are drawn in red. SSEs are drawn using Stride SSE assignments.Black arrows highlight particularly tight regions of the Kpax alignment compared to the TM-Align alignment.

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Protein Structure Alignment

Supplementary Figure 4. Structural alignment comparison between TM-Align and Kpaxusing six low sequence identity structures from Sippl andWeiderstein (2008), drawn in the same style as Supplementary Figure 3.

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Supplementary Figure 5. Structural alignment comparison between TM-Align and Kpaxusing six difficult structures from Gerstein and Levitt (1998), drawnin the same style as Supplementary Figure 3.

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Protein Structure Alignment

Supplementary Figure 6. Close-up view of the structural alignments calculated by TM-Align and Kpax for the pair 4aahA/1gofA from SupplementaryFigure 5 (drawn in the same style as Supplementary Figure 3).

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