D-SLIMMER: Domain–SLiM Interaction Motifs Miner for Sequence Based Protein–Protein Interaction Data
Copyright policy )D-SLIMMER: Domain–SLiM Interaction Motifs Miner for Sequence Based Protein–Protein Interaction Data
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.
- National University of Singapore Libraries Singapore
- Genome Institute of Singapore Singapore
- National University of Singapore Singapore
- Agency for Science, Technology and Research Singapore
- Institute for Infocomm Research Singapore
Amino Acid Motifs, Molecular Sequence Data, Computational Biology, Reproducibility of Results, domain-motif interaction, 551, short linear motif, protein-protein interaction, motif finding, Mice, Sequence Analysis, Protein, Protein Interaction Mapping, Animals, Data Mining, Humans, Protein Interaction Domains and Motifs, Amino Acid Sequence, Databases, Protein, Sequence Alignment, Algorithms, Software
Amino Acid Motifs, Molecular Sequence Data, Computational Biology, Reproducibility of Results, domain-motif interaction, 551, short linear motif, protein-protein interaction, motif finding, Mice, Sequence Analysis, Protein, Protein Interaction Mapping, Animals, Data Mining, Humans, Protein Interaction Domains and Motifs, Amino Acid Sequence, Databases, Protein, Sequence Alignment, Algorithms, Software
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