ArticleNucleic acids research2012
SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed, 122 citations in OpenAlex.
- ProteoCast: a web server to predict, validate, and interpret missense variant effects.Journal of molecular biology · 2026Article
- Short linear motifs-underexplored players drivingMicrobiology spectrum · 2026Article
- Proteome-wide prediction of the functional impact of missense variants with ProteoCast.Nature communications · 2026Article
- Pathogenic variations illuminate functional constraints in intrinsically disordered proteins.iScience · 2026Article
- Uncovering cancer dependencies in peptide-interacting protein pockets.bioRxiv : the preprint server for biology · 2026Article
- A proteome-wide dependency map of protein interaction motifs.Nature structural & molecular biology · 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
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- Training bias and sequence alignments shape protein-peptide docking by AlphaFold and related methods.Protein science : a publication of the Protein Society · 2025Article
- High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells.Nature communications · 2025Article
- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.Protein science : a publication of the Protein Society · 2025Article
- The Disorderly Nature of Caliciviruses.Viruses · 2024Review
- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.bioRxiv : the preprint server for biology · 2024Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Searching for EGF Fragments Recreating the Outer Sphere of the Growth Factor Involved in Receptor Interactions.International journal of molecular sciences · 2024Article
- xProtCAS: A Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures.Biomolecules · 2023Article
- Exploring the evolution and function of Canoe’s intrinsically disordered region in linking cell-cell junctions to the cytoskeleton during embryonic morphogenesis.bioRxiv : the preprint server for biology · 2023Article
- A Network-Based Approach for Improving Annotation of Transcription Factor Functions and Binding Sites inGenes · 2023Article
- Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
Abstract
Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.
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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 OpenQuestion graph.