ArticleNucleic acids research2017
SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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88 citing papers in PubMed.
- A practical guide to investigating biomolecular condensates: a comment from the plant community.Science China. Life sciences · 2026Review
- The extra-terminal domain drives the role of BET proteins in transcription.Nucleic acids research · 2026Article
- Predicting molecular recognition features in protein sequences with MoRFchibi 2.0.BMC bioinformatics · 2026Article
- Systematic discovery of motif-based interactions of the auxiliary domains of USP family deubiquitinases.Nature communications · 2026Article
- A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3.The Journal of biological chemistry · 2026Article
- Synthetic trap-peptides identify a TOM complex phosphatase - PP2A dephosphorylates Tom6.The FEBS journal · 2026Article
- SLiMs prediction method based on enhanced attention mechanism and feature fusion.Bioinformatics advances · 2026Article
- The non-catalytic DNA polymerase ε subunit is an NPF motif recognition protein.Nature communications · 2025Article
- Phosphatase specificity influences phosphorylation timing of CDK substrates during the cell cycle.Nature communications · 2025Article
- A simple workflow to identify novel small linear motif (SLiM)-mediated interactions with AlphaFold.Briefings in bioinformatics · 2025Article
- Dynamic intraligand binding reveals a new function for PDZ domains.Structure (London, England : 1993) · 2025Article
- Intrinsically disordered regions as facilitators of the transcription factor target search.Nature reviews. Genetics · 2025Review
- Elucidation of short linear motif-based interactions of the MIT and rhodanese domains of the ubiquitin-specific protease 8.Biology direct · 2025Article
- M-Motif, a potential non-conventional NLS in YAP/TAZ and other cellular and viral proteins that inhibits classic protein import.iScience · 2025Article
- The "DDVF" motif used by viral and bacterial proteins to hijack RSK kinases mimics a short linear motif (SLiM) found in proteins related to the RAS-ERK MAP kinase pathway.PLoS pathogens · 2025Article
- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.Protein science : a publication of the Protein Society · 2025Article
- Computational Prediction of Linear Interacting Peptides.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Enhancing prediction of short linear protein motifs with Wregex 3.0.Computational and structural biotechnology journal · 2024Article
- The RNA-dependent association of phosphatidylinositol 4,5-bisphosphate with intrinsically disordered proteins contribute to nuclear compartmentalization.PLoS genetics · 2024Article
- Subtleties in Clathrin heavy chain binding boxes provide selectivity among adaptor proteins of budding yeast.Nature communications · 2024Article
28 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
The extensive intrinsically disordered regions of higher eukaryotic proteomes contain vast numbers of functional interaction modules known as short linear motifs (SLiMs). Here, we present SLiMSearch, a motif discovery tool that scans a motif consensus, representing the specificity determinants of a motif-binding domain, against a proteome to discover putative novel motif instances. SLiMSearch applies several distinct and complementary approaches exploiting the common properties of SLiMs to predict novel motifs. Consensus matches are annotated with overlapping sequence annotation, including feature information describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterisation of functional regions. Discriminatory motif attributes such as conservation and accessibility are also calculated. In addition, SLiMSearch provides functional enrichment and evolutionary analysis tools. The enrichment tool analyses GO terms, keywords and interacting partner enrichment to indicate possible motif function. The evolutionary tool evaluates motif taxonomic range and the conservation of motif sequence context. Consensus matches can be filtered based on motif attributes such as accessibility and taxonomic range; or by the localisation, interacting partners or ontology annotation of the peptide-containing protein. SLiMSearch supports a range of species of experimental and therapeutic relevance and is available online at http://slim.ucd.ie/slimsearch/.
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