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Figure 1 | BMC Bioinformatics

Figure 1

From: FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures

Figure 1

Details of structural matches. Output page of a FunClust search in four non-homologous serine protease protein chains (1a0jA, 1sca, 1tyfA and 1e5tA). The three different clusters identified are shown in tabular form. For each cluster the associated score is reported. The right section of each table reports, in each row, the residues belonging to the different structures, with structurally aligned residues written in the same column. The left section shows the r.m.s.d. value for each match identified between the structures corresponding to the row and column of the table (recall that two structures belonging to the cluster do not necessarily match to each other). In the example shown, the first of the three clusters is composed of the four catalytic triads which are therefore correctly identified. The second cluster identifies three non-catalytic residues in structure 1e5t, while the third one (with the lowest score) involves only three of the four structures. A user activated popup window shows a graphical view (created using the Jmol applet) of the first cluster. The four different structures have been superposed on the residues belonging to the structural motif. Each structure has a different colour, and only the residues involved in the cluster are shown. Commands to trigger the display of the whole structure and of the labels for each protein in the cluster are located in the right portion of the window.

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