title: D-SLIMMER: domain-SLiM interaction motifs miner for sequence based protein-protein interaction data.
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.
authors: Department of Computer Science, National University of Singapore, 13 Computing Drive, 117417 Singapore.
authors: Willy
authors: W
authors: Hugo
authors: See-Kiong
authors: SK
authors: Ng
authors: Wing-Kin
authors: WK
authors: Sung
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping / Q000379:methods*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software