ArticleNucleic acids research2011
SLiMSearch 2.0: biological context for short linear motifs in proteins.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms.Genome biology and evolution · 2026Article
- SLiMs prediction method based on enhanced attention mechanism and feature fusion.Bioinformatics advances · 2026Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Comparative evaluation of AlphaFold2 and disorder predictors for prediction of intrinsic disorder, disorder content and fully disordered proteins.Computational and structural biotechnology journal · 2023Article
- Computational prediction of disordered binding regions.Computational and structural biotechnology journal · 2023Review
- Review
- Comparative study of the SBP-box gene family in rice siblings.Journal of biosciences · 2020Article
- Resources to Discover and Use Short Linear Motifs in Viral Proteins.Trends in biotechnology · 2020Review
- Analyzing the Sequences of Intrinsically Disordered Regions with CIDER and localCIDER.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX).Scientific reports · 2019Article
- Time-Frequency Approach Applied to Finding Interaction Regions in Pathogenic Proteins.Bioinformatics and biology insights · 2019Article
- The predictive performance of short-linear motif features in the prediction of calmodulin-binding proteins.BMC bioinformatics · 2018Article
- Peptides derived from cadherin juxtamembrane region inhibit platelet function.Royal Society open science · 2018Article
- Employing the one-cell C. elegans embryo to study cell division processes.Methods in cell biology · 2018Article
- Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins.Microbiome · 2017Article
- SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions.Nucleic acids research · 2017Article
- A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses.Virus genes · 2017Article
- Is unphosphorylated Rex, as multifunctional protein of HTLV-1, a fully intrinsically disordered protein? An in silico study.Biochemistry and biophysics reports · 2016Article
- Redefining the BH3 Death Domain as a 'Short Linear Motif'.Trends in biochemical sciences · 2015Review
- Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad.Cell communication and signaling : CCS · 2015Review
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Short, linear motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch 2.0 (Short, Linear Motif Search) web server allows researchers to identify occurrences of a user-defined SLiM in a proteome, using conservation and protein disorder context statistics to rank occurrences. User-friendly output and visualizations of motif context allow the user to quickly gain insight into the validity of a putatively functional motif occurrence. For each motif occurrence, overlapping UniProt features and annotated SLiMs are displayed. Visualization also includes annotated multiple sequence alignments surrounding each occurrence, showing conservation and protein disorder statistics in addition to known and predicted SLiMs, protein domains and known post-translational modifications. In addition, enrichment of Gene Ontology terms and protein interaction partners are provided as indicators of possible motif function. All web server results are available for download. Users can search motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html.
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