{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T12:32:47Z","timestamp":1744201967573},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: An important class of protein interactions involves the binding of a protein's domain to a short linear motif (SLiM) on its interacting partner. Extracting such motifs, either experimentally or computationally, is challenging because of their weak binding and high degree of degeneracy. Recent rapid increase of available protein structures provides an excellent opportunity to study SLiMs directly from their 3D structures.<\/jats:p>\n               <jats:p>Results: Using domain interface extraction (Diet), we characterized 452 distinct SLiMs from the Protein Data Bank (PDB), of which 155 are validated in varying degrees\u201440 have literature validation, 54 are supported by at least one domain\u2013peptide structural instance, and another 61 have overrepresentation in high-throughput PPI data. We further observed that the lacklustre coverage of existing computational SLiM detection methods could be due to the common assumption that most SLiMs occur outside globular domain regions. 198 of 452 SLiM that we reported are actually found on domain\u2013domain interface; some of them are implicated in autoimmune and neurodegenerative diseases. We suggest that these SLiMs would be useful for designing inhibitors against the pathogenic protein complexes underlying these diseases. Our findings show that 3D structure-based SLiM detection algorithms can provide a more complete coverage of SLiM-mediated protein interactions than current sequence-based approaches.<\/jats:p>\n               <jats:p>Contact: \u00a0ksung@comp.nus.edu.sg<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq065","type":"journal-article","created":{"date-parts":[[2010,2,19]],"date-time":"2010-02-19T01:45:29Z","timestamp":1266543929000},"page":"1036-1042","source":"Crossref","is-referenced-by-count":13,"title":["SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank"],"prefix":"10.1093","volume":"26","author":[{"given":"Willy","family":"Hugo","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, National University of Singapore, 13 Computing Drive S(117417), 2 Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, S(138632) and 3 Department of Information and Mathematical Science, Genome Institute of Singapore, 60 Biopolis Street, S(138672), Singapore"},{"name":"1 Department of Computer Science, National University of Singapore, 13 Computing Drive S(117417), 2 Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, S(138632) and 3 Department of Information and Mathematical Science, Genome Institute of Singapore, 60 Biopolis Street, S(138672), Singapore"}]},{"given":"Fushan","family":"Song","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, National University of Singapore, 13 Computing Drive S(117417), 2 Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, S(138632) and 3 Department of Information and Mathematical Science, Genome Institute of Singapore, 60 Biopolis Street, S(138672), Singapore"}]},{"given":"Zeyar","family":"Aung","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, National University of Singapore, 13 Computing Drive S(117417), 2 Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, S(138632) and 3 Department of Information and Mathematical Science, Genome Institute of Singapore, 60 Biopolis Street, S(138672), Singapore"}]},{"given":"See-Kiong","family":"Ng","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, National University of Singapore, 13 Computing Drive S(117417), 2 Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, S(138632) and 3 Department of Information and Mathematical Science, Genome Institute of Singapore, 60 Biopolis Street, S(138672), Singapore"}]},{"given":"Wing-Kin","family":"Sung","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, National University of Singapore, 13 Computing Drive S(117417), 2 Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, S(138632) and 3 Department of Information and Mathematical Science, Genome Institute of Singapore, 60 Biopolis Street, S(138672), Singapore"},{"name":"1 Department of Computer Science, National University of Singapore, 13 Computing Drive S(117417), 2 Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, S(138632) and 3 Department of Information and Mathematical Science, Genome Institute of Singapore, 60 Biopolis Street, S(138672), Singapore"}]}],"member":"286","published-online":{"date-parts":[[2010,2,18]]},"reference":[{"key":"2023012508080082400_B1","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1002\/(SICI)1097-0134(199607)25:3<354::AID-PROT7>3.0.CO;2-F","article-title":"Analysis of topological and nontopological structural similarities in the PDB: new examples with old structures","volume":"25","author":"Alexandrov","year":"1996","journal-title":"Proteins"},{"key":"2023012508080082400_B2","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1038\/nrm1859","article-title":"Structural systems biology: modelling protein interactions","volume":"7","author":"Aloy","year":"2006","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023012508080082400_B3","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gkm993","article-title":"Data growth and its impact on the SCOP database: new developments","volume":"36","author":"Andreeva","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012508080082400_B4","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1142\/S0219720006002417","article-title":"MatAlign: precise protein structure comparison by matrix alignment","volume":"4","author":"Aung","year":"2006","journal-title":"J. Bioinform. Comput. Biol."},{"key":"2023012508080082400_B5","doi-asserted-by":"crossref","first-page":"D175","DOI":"10.1038\/nmeth856","article-title":"MiniMotif miner: a tool for investigating protein function","volume":"3","author":"Balla","year":"2006","journal-title":"Nat. Methods"},{"key":"2023012508080082400_B6","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkh121","article-title":"The Pfam protein families database","volume":"32","author":"Bateman","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012508080082400_B7","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023012508080082400_B8","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1002\/(SICI)1097-4547(20000415)60:2<150::AID-JNR3>3.0.CO;2-4","article-title":"Glyceraldehyde-3-phosphate dehydrogenase and apoptosis","volume":"60","author":"Berry","year":"2000","journal-title":"J. Neurosci. Res."},{"key":"2023012508080082400_B9","doi-asserted-by":"crossref","first-page":"e182","DOI":"10.1371\/journal.pcbi.0030182","article-title":"Structure-templated predictions of novel protein interactions from sequence information","volume":"3","author":"Betel","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"2023012508080082400_B10","doi-asserted-by":"crossref","first-page":"12254","DOI":"10.1073\/pnas.0803556105","article-title":"Crystal structures of fibronectin-binding sites from Staphylococcus aureus FnBPA in complex with fibronectin domains","volume":"105","author":"Bingham","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508080082400_B11","doi-asserted-by":"crossref","first-page":"D637","DOI":"10.1093\/nar\/gkm1001","article-title":"The BioGRID interaction database: 2008 update","volume":"36","author":"Breitkreutz","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012508080082400_B12","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1016\/S0959-440X(98)80101-2","article-title":"Conformational changes and disease-serpins, prions and Alzheimer's","volume":"8","author":"Carrell","year":"1998","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023012508080082400_B13","doi-asserted-by":"crossref","first-page":"D310","DOI":"10.1093\/nar\/gkn877","article-title":"The CATH classification revisited\u2014architectures reviewed and new ways to characterize structural divergence in superfamilies","volume":"37","author":"Cuff","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012508080082400_B14","doi-asserted-by":"crossref","first-page":"1486","DOI":"10.1093\/bioinformatics\/bth106","article-title":"Using convex hulls to extract interaction interfaces from known structures","volume":"20","author":"Dafas","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012508080082400_B15","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"2023012508080082400_B16","doi-asserted-by":"crossref","first-page":"e967","DOI":"10.1371\/journal.pone.0000967","article-title":"SLiMFinder: a probabilistic method for identifying overrepresented, convergently evolved, short linear motifs in proteins","volume":"2","author":"Edwards","year":"2007","journal-title":"PLoS ONE"},{"key":"2023012508080082400_B17","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1093\/bioinformatics\/15.6.480","article-title":"A comparison of sequence and structure protein domain families as a basis for structural genomics","volume":"15","author":"Elofsson","year":"1999","journal-title":"Bioinformatics"},{"key":"2023012508080082400_B18","doi-asserted-by":"crossref","first-page":"2049","DOI":"10.1097\/00001756-200107030-00051","article-title":"GAPDH knockdown rescues mesencephalic dopaminergic neurons from MPP+ induced apoptosis","volume":"42","author":"Fukuhara","year":"2001","journal-title":"Neuroreport"},{"key":"2023012508080082400_B19","doi-asserted-by":"crossref","first-page":"5977","DOI":"10.1021\/bi034017g","article-title":"BAFF\/BLyS receptor 3 comprises a minimal TNF receptor-like module that encodes a highly focused ligand-binding site","volume":"42","author":"Gordon","year":"2003","journal-title":"Biochemistry"},{"key":"2023012508080082400_B20","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1038\/35010115","article-title":"TACI and BCMA are receptors for a TNF homologue implicated in B-cell autoimmune disease","volume":"404","author":"Gross","year":"2000","journal-title":"Nature"},{"key":"2023012508080082400_B21","doi-asserted-by":"crossref","first-page":"10915","DOI":"10.1073\/pnas.89.22.10915","article-title":"Amino acid substitution matrices from protein blocks","volume":"89","author":"Henikoff","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508080082400_B22","doi-asserted-by":"crossref","first-page":"3370","DOI":"10.1073\/pnas.97.7.3370","article-title":"Severe B cell hyperplasia and autoimmune disease in TALL-1 transgenic mice","volume":"97","author":"Khare","year":"2000","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508080082400_B23","doi-asserted-by":"crossref","first-page":"e124","DOI":"10.1371\/journal.pcbi.0020124","article-title":"The many faces of protein\u2013protein interactions: a compendium of interface geometry","volume":"2","author":"Kim","year":"2006","journal-title":"PLoS Comput. Biol."},{"key":"2023012508080082400_B24","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1093\/bioinformatics\/btl020","article-title":"Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012508080082400_B25","doi-asserted-by":"crossref","first-page":"3437","DOI":"10.1073\/pnas.95.7.3437","article-title":"The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-\u00c5 resolution","volume":"95","author":"Liu","year":"1998","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508080082400_B26","first-page":"989","article-title":"A domain-swapped RNase a dimer with implications for amyloid formation","volume":"8","author":"Liu","year":"2001","journal-title":"Nat. Struct. Biol."},{"key":"2023012508080082400_B27","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/nature750","article-title":"Comparative assessment of large-scale data sets of protein\u2013protein interactions","volume":"417","author":"von Mering","year":"2002","journal-title":"Nature"},{"key":"2023012508080082400_B28","doi-asserted-by":"crossref","first-page":"4821","DOI":"10.1021\/bi00520a003","article-title":"Effect of macromolecular crowding upon the structure and function of an enzyme: glyceraldehyde-3-phosphate dehydrogenase","volume":"20","author":"Minton","year":"1981","journal-title":"Biochemistry"},{"key":"2023012508080082400_B29","doi-asserted-by":"crossref","first-page":"e405","DOI":"10.1371\/journal.pbio.0030405","article-title":"Systematic discovery of new recognition peptides mediating protein interaction networks","volume":"3","author":"Neduva","year":"2005","journal-title":"PLoS Biol."},{"key":"2023012508080082400_B30","doi-asserted-by":"crossref","first-page":"3342","DOI":"10.1016\/j.febslet.2005.04.005","article-title":"Linear motifs: evolutionary interaction switches","volume":"579","author":"Neduva","year":"2005","journal-title":"FEBS Lett."},{"key":"2023012508080082400_B31","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/j.copbio.2006.08.002","article-title":"Peptides mediating interaction networks: new leads at last","volume":"17","author":"Neduva","year":"2006","journal-title":"Curr. Opin. Biotechnol."},{"key":"2023012508080082400_B32","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1126\/science.1083653","article-title":"Assembly of cell regulatory systems through protein interaction domains","volume":"300","author":"Pawson","year":"2003","journal-title":"Science"},{"key":"2023012508080082400_B33","doi-asserted-by":"crossref","first-page":"3625","DOI":"10.1093\/nar\/gkg545","article-title":"ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins","volume":"31","author":"Puntervoll","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012508080082400_B34","volume-title":"Information Retrieval.","author":"Rijsbergen","year":"1979"},{"key":"2023012508080082400_B35","doi-asserted-by":"crossref","first-page":"6059","DOI":"10.1073\/pnas.94.12.6059","article-title":"Three-dimensional solution structure of the complex of alpha-bungarotoxin with a library-derived peptide","volume":"94","author":"Scherf","year":"1997","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508080082400_B36","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1186\/1471-2105-7-502","article-title":"A correlated motif approach for finding short linear motifs from protein interaction networks","volume":"7","author":"Tan","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012508080082400_B37","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1007\/s00702-002-0827-z","article-title":"Neuroprotection by deprenyl and other propargylamines: glyceraldehyde-3-phosphate dehydrogenase rather than monoamine oxidase B","volume":"110","author":"Tatton","year":"2003","journal-title":"J. Neural Transm."},{"key":"2023012508080082400_B38","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/1471-2105-9-9","article-title":"SCOWLP classification: structural comparison and analysis of protein binding regions","volume":"9","author":"Teyra","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012508080082400_B39","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/j.jmb.2005.01.044","article-title":"Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families","volume":"347","author":"Torrance","year":"2005","journal-title":"J. Mol. Biol."},{"key":"2023012508080082400_B40","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1186\/1471-2105-10-351","article-title":"A structure filter for the Eukaryotic Linear Motif Resource","volume":"10","author":"Via","year":"2009","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/8\/1036\/48856898\/bioinformatics_26_8_1036.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/8\/1036\/48856898\/bioinformatics_26_8_1036.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:12:05Z","timestamp":1674634325000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/8\/1036\/205449"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,2,18]]},"references-count":40,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2010,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq065","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,4,15]]},"published":{"date-parts":[[2010,2,18]]}}}