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. 2006 Oct 25;35(Database issue):D317–D321. doi: 10.1093/nar/gkl809

Figure 1.

Figure 1

(A) Initial output page (web-browser) shown from a search using protein 1s12 chain C, all values from T-DB are shown in table format, by selecting the ‘ALIGN’ button, a new browser is opened showing the alignment plot, sequence alignment, and initializing the Friend Applet. (B) Friend Applet demonstrating the TOPOFIT superimposition (backbone representation) between Human Frataxin (PDB-code ‘1ekg’ chain A, blue) and Hypothetical Protein TM1457 (PDB-code ‘1s12’ chain C, green), Ne 74, RMSD 1.8 Å. (C) An example of a non-sequential alignment found by the TOPOFIT method, the alignment plot between 1ekg chain A (x-axis) and 1s12 chain C (y-axis) is shown, notice the three reverse fragments (dotted circles).