ArticleScience signaling2012
Proteome-wide discovery of evolutionary conserved sequences in disordered regions.
Article in Science signaling, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- ProteoCast: a web server to predict, validate, and interpret missense variant effects.Journal of molecular biology · 2026Article
- Sequence Conservation and Functional Significance of Charged Clusters in Mitochondria-Located Proteins of Green Plants.Journal of molecular evolution · 2026Article
- Multi-Omics Dissection of the Shared Genetic Architecture Between Sleep Traits and Epilepsy.Biology · 2026Article
- Proteome-wide prediction of the functional impact of missense variants with ProteoCast.Nature communications · 2026Article
- Sequence and chemical specificity define the functional landscape of intrinsically disordered regions.Nature cell biology · 2026Article
- Molecular grammars of predicted intrinsically disordered regions that span the human proteome.Cell · 2026Article
- Elucidating the susceptibility genes between insomnia and migraine by integrating genetic data and transcriptomes.The journal of headache and pain · 2026Article
- STARD9 and CDK5RAP2-Novel Candidate Genes for 46,XY Complete Gonadal Dysgenesis.International journal of molecular sciences · 2025Article
- Article
- Intrinsically disordered regions as facilitators of the transcription factor target search.Nature reviews. Genetics · 2025Review
- Bridging prediction and reality: Comprehensive analysis of experimental and AlphaFold 2 full-length nuclear receptor structures.Computational and structural biotechnology journal · 2025Article
- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.Protein science : a publication of the Protein Society · 2025Article
- SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.bioRxiv : the preprint server for biology · 2024Article
- A complete map of specificity encoding for a partially fuzzy protein interaction.bioRxiv : the preprint server for biology · 2024Article
- Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation.PLoS computational biology · 2024Article
- Direct prediction of intrinsically disordered protein conformational properties from sequence.Nature methods · 2024Article
- Proteome-wide assessment of human interactome as a source of capturing domain-motif and domain-domain interactions.Journal of cell communication and signaling · 2024Article
- Pathogenic Variants inInternational journal of molecular sciences · 2023Article
- A computational framework for resolving the microbiome diversity conundrum.Nature communications · 2023Article
23 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
At least 30% of human proteins are thought to contain intrinsically disordered regions, which lack stable structural conformation. Despite lacking enzymatic functions and having few protein domains, disordered regions are functionally important for protein regulation and contain short linear motifs (short peptide sequences involved in protein-protein interactions), but in most disordered regions, the functional amino acid residues remain unknown. We searched for evolutionarily conserved sequences within disordered regions according to the hypothesis that conservation would indicate functional residues. Using a phylogenetic hidden Markov model (phylo-HMM), we made accurate, specific predictions of functional elements in disordered regions even when these elements are only two or three amino acids long. Among the conserved sequences that we identified were previously known and newly identified short linear motifs, and we experimentally verified key examples, including a motif that may mediate interaction between protein kinase Cbk1 and its substrates. We also observed that hub proteins, which interact with many partners in a protein interaction network, are highly enriched in these conserved sequences. Our analysis enabled the systematic identification of the functional residues in disordered regions and suggested that at least 5% of amino acids in disordered regions are important for function.
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