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Title: D-SLIMMER: Domain-SLiM interaction motifs miner for sequence based protein-protein interaction data
Authors: Hugo, W. 
Ng, S.-K.
Sung, W.-K. 
Keywords: domain-motif interaction
motif finding
protein-protein interaction
short linear motif
Issue Date: 2011
Citation: Hugo, W., Ng, S.-K., Sung, W.-K. (2011). D-SLIMMER: Domain-SLiM interaction motifs miner for sequence based protein-protein interaction data. Journal of Proteome Research 10 (12) : 5285-5295. ScholarBank@NUS Repository.
Abstract: Many biologically important protein-protein interactions (PPIs) have been found to be mediated by short linear motifs (SLiMs). These interactions are mediated by the binding of a protein domain, often with a nonlinear interaction interface, to a SLiM. We propose a method called D-SLIMMER to mine for SLiMs in PPI data on the basis of the interaction density between a nonlinear motif (i.e., a protein domain) in one protein and a SLiM in the other protein. Our results on a benchmark of 113 experimentally verified reference SLiMs showed that D-SLIMMER outperformed existing methods notably for discovering domain-SLiMs interaction motifs. To illustrate the significance of the SLiMs detected, we highlighted two SLiMs discovered from the PPI data by D-SLIMMER that are variants of the known ELM SLiM, as well as a literature-backed SLiM that is yet to be listed in the reference databases. We also presented a novel SLiM predicted by D-SLIMMER that was strongly supported by existing biological literatures. These examples showed that D-SLIMMER is able to find SLiMs that are biologically relevant. © 2011 American Chemical Society.
Source Title: Journal of Proteome Research
ISSN: 15353893
DOI: 10.1021/pr200312e
Appears in Collections:Staff Publications

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