ArticleBioinformatics (Oxford, England)2012
The identification of short linear motif-mediated interfaces within the human interactome.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 72 citations in OpenAlex.
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- Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing.Nature communications · 2024Article
- Phase separations in oncogenesis, tumor progressions and metastasis: a glance from hallmarks of cancer.Journal of hematology & oncology · 2023Review
- Sequence variations of phase-separating proteins and resources for studying biomolecular condensates.Acta biochimica et biophysica Sinica · 2023Review
- Digging into the 3D Structure Predictions of AlphaFold2 with Low Confidence: Disorder and Beyond.Biomolecules · 2022Article
- Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates.Scientific reports · 2022Article
- Host PDZ-containing proteins targeted by SARS-CoV-2.The FEBS journal · 2021Article
- Studying the Structures of Relaxed and Fuzzy Interactions: The Diverse World of S100 Complexes.Frontiers in molecular biosciences · 2021Review
- PDZ Sample Quality Assessment by Biochemical and Biophysical Characterizations.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway.PLoS computational biology · 2017Article
- Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins.Microbiome · 2017Article
- Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks.Scientific reports · 2017Article
- SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions.Nucleic acids research · 2017Article
- Quantifying domain-ligand affinities and specificities by high-throughput holdup assay.Nature methods · 2015Article
- Predicting peptide-mediated interactions on a genome-wide scale.PLoS computational biology · 2015Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationEukaryotic 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.
resultsIn 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.de CONTACT: toby.gibson@embl.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.