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.2008 Mar 26;9 Suppl 2(Suppl 2):S2.
doi: 10.1186/1471-2105-9-S2-S2.

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

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

Gabriele Ausiello et al. BMC Bioinformatics..

Abstract

Background: The occurrence of very similar structural motifs brought about by different parts of non homologous proteins is often indicative of a common function. Indeed, relatively small local structures can mediate binding to a common partner, be it a protein, a nucleic acid, a cofactor or a substrate. While it is relatively easy to identify short amino acid or nucleotide sequence motifs in a given set of proteins or genes, and many methods do exist for this purpose, much more challenging is the identification of common local substructures, especially if they are formed by non consecutive residues in the sequence.

Results: Here we describe a publicly available tool, able to identify common structural motifs shared by different non homologous proteins in an unsupervised mode. The motifs can be as short as three residues and need not to be contiguous or even present in the same order in the sequence. Users can submit a set of protein structures deemed or not to share a common function (e.g. they bind similar ligands, or share a common epitope). The server finds and lists structural motifs composed of three or more spatially well conserved residues shared by at least three of the submitted structures. The method uses a local structural comparison algorithm to identify subsets of similar amino acids between each pair of input protein chains and a clustering procedure to group similarities shared among different structure pairs.

Conclusions: FunClust is fast, completely sequence independent, and does not need an a priori knowledge of the motif to be found. The output consists of a list of aligned structural matches displayed in both tabular and graphical form. We show here examples of its usefulness by searching for the largest common structural motifs in test sets of non homologous proteins and showing that the identified motifs correspond to a known common functional feature.

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Figures

Figure 1
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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