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. 2013 Jul;41(Web Server issue):W358-62.
doi: 10.1093/nar/gkt383. Epub 2013 May 28.

T-RMSD: a web server for automated fine-grained protein structural classification

Cedrik Magis  1 , Paolo Di Tommaso, Cedric Notredame
Affiliations

T-RMSD: a web server for automated fine-grained protein structural classification

Cedrik Magis et al. Nucleic Acids Res. 2013 Jul.

Abstract

This article introduces the T-RMSD web server (tree-based on root-mean-square deviation), a service allowing the online computation of structure-based protein classification. It has been developed to address the relation between structural and functional similarity in proteins, and it allows a fine-grained structural clustering of a given protein family or group of structurally related proteins using distance RMSD (dRMSD) variations. These distances are computed between all pairs of equivalent residues, as defined by the ungapped columns within a given multiple sequence alignment. Using these generated distance matrices (one per equivalent position), T-RMSD produces a structural tree with support values for each cluster node, reminiscent of bootstrap values. These values, associated with the tree topology, allow a quantitative estimate of structural distances between proteins or group of proteins defined by the tree topology. The clusters thus defined have been shown to be structurally and functionally informative. The T-RMSD web server is a free website open to all users and available at http://tcoffee.crg.cat/apps/tcoffee/do:trmsd.

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Figures

Figure 1.
Figure 1.
Sample T-RMSD result page. (a) The MSA colored according to T-RMSD color scheme where ungapped columns in red correspond to highly discriminant positions and blue correspond to poorly discriminant one. The color scheme represents the individual contribution to each ungapped column in generating the final clustering: positions structurally highly conserved among all proteins will have low contribution in discriminating structural variations. For post-processing purpose, users are advised to download the text-based version of the alignment available in the ‘Result File’ section. (b) The structural clustering generated by the T-RMSD method displayed using the jsPhyloSVG library. The values at each node, analog to bootstrap values, represent the support of the split. (c) The template section where the template file and the list of structure files used for the computation can be visualized.
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