ArticleBioinformatics (Oxford, England)2015
QSLiMFinder: improved short linear motif prediction using specific query protein data.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Predicting molecular recognition features in protein sequences with MoRFchibi 2.0.BMC bioinformatics · 2026Article
- mimicDetector: a pipeline for protein motif mimicry detection in host-pathogen interactions.Bioinformatics (Oxford, England) · 2026Article
- SLiMs prediction method based on enhanced attention mechanism and feature fusion.Bioinformatics advances · 2026Article
- Computational Prediction of Linear Interacting Peptides.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Prediction of motif-mediated viral mimicry through the integration of host-pathogen interactions.Archives of microbiology · 2024Article
- Interaction modules that impart specificity to disordered protein.Trends in biochemical sciences · 2023Review
- Emergence of terpene chemical communication in insects: Evolutionary recruitment of isoprenoid metabolism.Protein science : a publication of the Protein Society · 2023Article
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Computational prediction of disordered binding regions.Computational and structural biotechnology journal · 2023Review
- How different viruses perturb host cellular machinery via short linear motifs.EXCLI journal · 2023Review
- Structure and Dynamics in the ATG8 Family From Experimental to Computational Techniques.Frontiers in cell and developmental biology · 2020Review
- The eukaryotic linear motif resource - 2018 update.Nucleic acids research · 2018Article
- Article
- A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses.Virus genes · 2017Article
- Article
- SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks.F1000Research · 2015Article
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Authors and funding
3 authors.
Funding
Abstract
motivationThe sensitivity of de novo short linear motif (SLiM) prediction is limited by the number of patterns (the motif space) being assessed for enrichment. QSLiMFinder uses specific query protein information to restrict the motif space and thereby increase the sensitivity and specificity of predictions.
resultsQSLiMFinder was extensively benchmarked using known SLiM-containing proteins and simulated protein interaction datasets of real human proteins. Exploiting prior knowledge of a query protein likely to be involved in a SLiM-mediated interaction increased the proportion of true positives correctly returned and reduced the proportion of datasets returning a false positive prediction. The biggest improvement was seen if a short region of the query protein flanking the interaction site was known. AVAILABILITY AND IMPLEMENTATION: All the tools and data used in this study, including QSLiMFinder and the SLiMBench benchmarking software, are freely available under a GNU license as part of SLiMSuite, at: http://bioware.soton.ac.uk.
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