ArticleNucleic acids research2010
SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Systematic discovery of motif-based interactions of the auxiliary domains of USP family deubiquitinases.Nature communications · 2026Article
- SHARK-capture identifies functional motifs in intrinsically disordered protein regions.Protein science : a publication of the Protein Society · 2025Article
- Article
- Prediction of motif-mediated viral mimicry through the integration of host-pathogen interactions.Archives of microbiology · 2024Article
- Motif-dependent binding on the intervening domain regulates O-GlcNAc transferase.Nature chemical biology · 2023Article
- Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets.Nature communications · 2023Article
- Elucidation of Short Linear Motif-Based Interactions of the FERM Domains of Ezrin, Radixin, Moesin, and Merlin.Biochemistry · 2023Article
- A novel binding site on the cryptic intervening domain is a motif-dependent regulator of O-GlcNAc transferase.Research square · 2023Article
- Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.Molecular systems biology · 2022Article
- Dynamic, but Not Necessarily Disordered, Human-Virus Interactions Mediated through SLiMs in Viral Proteins.Viruses · 2021Review
- Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs.Current research in structural biology · 2021Article
- Article
- Resources to Discover and Use Short Linear Motifs in Viral Proteins.Trends in biotechnology · 2020Review
- Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology.Trends in biochemical sciences · 2019Review
- The predictive performance of short-linear motif features in the prediction of calmodulin-binding proteins.BMC bioinformatics · 2018Article
- Exhaustive search of linear information encoding protein-peptide recognition.PLoS computational biology · 2017Article
- Evolutionary conservation of Ebola virus proteins predicts important functions at residue level.Bioinformatics (Oxford, England) · 2017Article
- Article
- 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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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Short, linear motifs (SLiMs) play a critical role in many biological processes, particularly in protein-protein interactions. The Short, Linear Motif Finder (SLiMFinder) web server is a de novo motif discovery tool that identifies statistically over-represented motifs in a set of protein sequences, accounting for the evolutionary relationships between them. Motifs are returned with an intuitive P-value that greatly reduces the problem of false positives and is accessible to biologists of all disciplines. Input can be uploaded by the user or extracted directly from UniProt. Numerous masking options give the user great control over the contextual information to be included in the analyses. The SLiMFinder server combines these with user-friendly output and visualizations of motif context to allow the user to quickly gain insight into the validity of a putatively functional motif. These visualizations include alignments of motif occurrences, alignments of motifs and their homologues and a visual schematic of the top-ranked motifs. Returned motifs can also be compared with known SLiMs from the literature using CompariMotif. All results are available for download. The SLiMFinder server is available at: http://bioware.ucd.ie/slimfinder.html.
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Registered trials
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 OpenQuestion graph.