biostudies-literatureUnknown6Idrees SUniversity International Postgraduate Award to Sobia IdreesMany important cellular processes involve protein-protein interactions (PPIs) mediated by a Short Linear Motif (SLiM) in one protein interacting with a globular domain in another. Despite their significance, these domain-motif interactions (DMIs) are typically low affinity, which makes them challenging to identify by classical experimental approaches, such as affinity pulldown mass spectrometry (AP-MS) and yeast two-hybrid (Y2H). DMIs are generally underrepresented in PPI networks as a result. A number of computational methods now exist to predict SLiMs and/or DMIs from experimental interaction data but it is yet to be established how effective different PPI detection methods are for capturing these low affinity SLiM-mediated interactions. Here, we introduce a new computational pipeline (SPeerJe5858https://www.ebi.ac.uk/biostudies/studies/S-EPMC6215436biostudies-literatureSLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions.PMC6215436Idrees SPerez-Bercoff AEdwards RJfalseSLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions.Many important cellular processes involve protein-protein interactions (PPIs) mediated by a Short Linear Motif (SLiM) in one protein interacting with a globular domain in another. Despite their significance, these domain-motif interactions (DMIs) are typically low affinity, which makes them challenging to identify by classical experimental approaches, such as affinity pulldown mass spectrometry (AP-MS) and yeast two-hybrid (Y2H). DMIs are generally underrepresented in PPI networks as a result. A number of computational methods now exist to predict SLiMs and/or DMIs from experimental interaction data but it is yet to be established how effective different PPI detection methods are for capturing these low affinity SLiM-mediated interactions. Here, we introduce a new computational pipeline (S2018-01-01T00:00:00Z20182025-04-04T09:14:48.219Z2019-03-27T00:06:14ZS-EPMC62154363040235210.7717/peerj.5858