Dataset Information
The identification of short linear motif-mediated interfaces within the human interactome.
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ABSTRACT: Motivation
Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein-protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by short linear motifs (SLiMs), particularly the canonical and ubiquitous SH2, SH3 and PDZ domain-binding motifs. However, these motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of motif instances.Results
In this article, interaction data are analysed to identify and characterize an important subset of PPIs, those involving SLiMs binding to globular domains. To do this, we introduce iELM, a method to identify interactions mediated by SLiMs and add molecular details of the interaction interfaces to both interacting proteins. The method identifies SLiM-mediated interfaces from PPI data by searching for known SLiM-domain pairs. This approach was applied to the human interactome to identify a set of high-confidence putative SLiM-mediated PPIs.Availability
iELM is freely available at http://elmint.embl.deContact
toby.gibson@embl.deSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Weatheritt RJ
PROVIDER: S-EPMC3315716 | biostudies-literature | 2012 Apr
REPOSITORIES: biostudies-literature
Publications
The identification of short linear motif-mediated interfaces within the human interactome.
Bioinformatics (Oxford, England) 20120210 7
<h4>Motivation</h4>Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein-protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by short li ...[more]