{"doi":"10.1093/nar/gks854","title":"SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions","abstract":null,"journal":"Nucleic Acids Research","year":2012,"id":628756,"datarank":0.7242470605953454,"base_score":4.8283137373023015,"endowment":4.8283137373023015,"self_citation_contribution":0.7242470605953454,"citation_network_contribution":0.0,"self_endowment_contribution":0.7242470605953454,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":124,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1628055,"name":"Joanne L. Cowan","orcid":null,"position":1,"is_corresponding":false},{"id":607675,"name":"Denis C. Shields","orcid":"0000-0003-4015-2474","position":2,"is_corresponding":false},{"id":28917,"name":"Toby J. Gibson","orcid":"0000-0003-0657-5166","position":3,"is_corresponding":false},{"id":137844,"name":"Mark J. Coldwell","orcid":null,"position":4,"is_corresponding":false},{"id":113079,"name":"Richard J. Edwards","orcid":null,"position":5,"is_corresponding":false},{"id":293148,"name":"Norman E. Davey","orcid":"0000-0001-6988-4850","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions","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.","is_dataset_classified":null,"base_score":4.8283137373023015,"endowment":4.8283137373023015,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"22977176","pmcid":"PMC3510515","openalex_id":"https://openalex.org/W1996543580","authors":[],"funders":[{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/H006834/1","title":"Mechanisms of alternative translation initiation codon selection in the regulation of eukaryotic gene expression"},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/I006230/1","title":"Integrated in silico prediction of protein interaction motifs using interactome networks and high-resolution 3-dimensional structures"},{"funder_name":"Science Foundation Ireland","grant_id":"08/IN.1/B1864","title":"Towards the druggable interactome: bioinformatic analysis of protein interactions and oligopeptide modulation of signalling networks"}],"total_grants":3,"fwci":3.616,"citation_percentile":0.93634415,"influential_citations":0,"citation_trend":[{"year":2012,"count":1},{"year":2013,"count":8},{"year":2014,"count":13},{"year":2015,"count":6},{"year":2016,"count":6},{"year":2017,"count":19},{"year":2018,"count":8},{"year":2019,"count":4},{"year":2020,"count":7},{"year":2021,"count":11},{"year":2022,"count":4},{"year":2023,"count":9},{"year":2024,"count":9},{"year":2025,"count":11},{"year":2026,"count":8}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/40/21/10628/25347829/gks854.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/40/21/10628/25347829/gks854.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/40/21/10628/16961134/gks854.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gks854","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/22977176","host_type":"repository"},{"url":"http://nar.oxfordjournals.org/cgi/content/short/40/21/10628","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3510515","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC3510515","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC3510515?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1093/nar/gks854","host_type":""},{"url":"https://dx.doi.org/10.1093/nar/gks854","host_type":""},{"url":"https://doi.org/https://doi.org/10.1093/nar/gks854","host_type":""}],"fields_of_study":["Cellular transport and secretion","Fungal and yeast genetics research","RNA and protein synthesis mechanisms","0301 basic medicine","0303 health sciences","03 medical and health sciences","Adaptor Proteins, Vesicular Transport","Amino Acid Motifs","Amino Acid Sequence","Conserved Sequence","Eukaryotic Initiation Factor-2","Eukaryotic Initiation Factor-4E","F-Box Proteins","HeLa Cells","Humans","Molecular Sequence Data","Probability","Proteome","Sequence Alignment","Sequence Analysis, Protein"],"mesh_terms":["Amino Acid Sequence","HeLa Cells","Humans","Molecular Sequence Data","Probability","Eukaryotic Initiation Factor-2","Sequence Alignment","Conserved Sequence","Sequence Analysis, Protein","Proteome","Amino Acid Motifs","Adaptor Proteins, Vesicular Transport","Eukaryotic Initiation Factor-4E","F-Box Proteins","Hela Cells"],"keywords":["Biology","Computational biology","Motif (music)","Proteome","Conserved sequence","Sequence motif","Structural motif","Human proteome project","Intrinsically disordered proteins","Sequence alignment","Drug discovery","Genetics","Evolutionary biology","Bioinformatics","Proteomics","Peptide sequence","Gene","Biochemistry","F-Box Proteins","Amino Acid Motifs","Eukaryotic Initiation Factor-2","Molecular Sequence Data","610","Adaptor Proteins, Vesicular Transport","Eukaryotic Initiation Factor-4E","Sequence Analysis, Protein","Humans","Amino Acid Sequence","HeLa Cells","Probability"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Reduced inequalities"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"},{"name":"uniprot"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-05T14:56:38.819617Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}