{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T00:37:42Z","timestamp":1767919062635,"version":"3.49.0"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1696,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein\u2013protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by short linear motifs (SLiMs), particularly the canonical and ubiquitous SH2, SH3 and PDZ domain-binding motifs. However, these motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of motif instances.<\/jats:p>\n               <jats:p>Results: In this article, interaction data are analysed to identify and characterize an important subset of PPIs, those involving SLiMs binding to globular domains. To do this, we introduce iELM, a method to identify interactions mediated by SLiMs and add molecular details of the interaction interfaces to both interacting proteins. The method identifies SLiM-mediated interfaces from PPI data by searching for known SLiM\u2013domain pairs. This approach was applied to the human interactome to identify a set of high-confidence putative SLiM-mediated PPIs.<\/jats:p>\n               <jats:p>Availability: iELM is freely available at http:\/\/elmint.embl.de<\/jats:p>\n               <jats:p>Contact: \u00a0toby.gibson@embl.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts072","type":"journal-article","created":{"date-parts":[[2012,2,11]],"date-time":"2012-02-11T04:47:14Z","timestamp":1328935634000},"page":"976-982","source":"Crossref","is-referenced-by-count":61,"title":["The identification of short linear motif-mediated interfaces within the human interactome"],"prefix":"10.1093","volume":"28","author":[{"given":"R. J.","family":"Weatheritt","sequence":"first","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2Group Oncoproteins, Unit\u00e9 CNRS-UDS UMR 7242, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, Bd S\u00e9bastien Brant, BP 10413, 67412 Illkirch - Cedex, France, 3Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, 4Department of Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 5Chemical Biology Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"K.","family":"Luck","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2Group Oncoproteins, Unit\u00e9 CNRS-UDS UMR 7242, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, Bd S\u00e9bastien Brant, BP 10413, 67412 Illkirch - Cedex, France, 3Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, 4Department of Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 5Chemical Biology Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E.","family":"Petsalaki","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2Group Oncoproteins, Unit\u00e9 CNRS-UDS UMR 7242, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, Bd S\u00e9bastien Brant, BP 10413, 67412 Illkirch - Cedex, France, 3Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, 4Department of Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 5Chemical Biology Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"},{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2Group Oncoproteins, Unit\u00e9 CNRS-UDS UMR 7242, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, Bd S\u00e9bastien Brant, BP 10413, 67412 Illkirch - Cedex, France, 3Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, 4Department of Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 5Chemical Biology Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"N. E.","family":"Davey","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2Group Oncoproteins, Unit\u00e9 CNRS-UDS UMR 7242, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, Bd S\u00e9bastien Brant, BP 10413, 67412 Illkirch - Cedex, France, 3Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, 4Department of Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 5Chemical Biology Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"},{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2Group Oncoproteins, Unit\u00e9 CNRS-UDS UMR 7242, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, Bd S\u00e9bastien Brant, BP 10413, 67412 Illkirch - Cedex, France, 3Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, 4Department of Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 5Chemical Biology Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"T. J.","family":"Gibson","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2Group Oncoproteins, Unit\u00e9 CNRS-UDS UMR 7242, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 1, Bd S\u00e9bastien Brant, BP 10413, 67412 Illkirch - Cedex, France, 3Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, 4Department of Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 5Chemical Biology Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,2,10]]},"reference":[{"key":"2023012512241488400_B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023012512241488400_B2","doi-asserted-by":"crossref","first-page":"e26","DOI":"10.1371\/journal.pcbi.0010026","article-title":"Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions","volume":"1","author":"Beltrao","year":"2005","journal-title":"PLoS Comput. Biol."},{"key":"2023012512241488400_B3","doi-asserted-by":"crossref","first-page":"1783","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":"2023012512241488400_B4","doi-asserted-by":"crossref","first-page":"W444","DOI":"10.1093\/nar\/gkn336","article-title":"NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways","volume":"36","author":"Brohee","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B5","doi-asserted-by":"crossref","first-page":"D557","DOI":"10.1093\/nar\/gkl961","article-title":"DOMINO: a database of domain-peptide interactions","volume":"35","author":"Ceol","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B6","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1186\/1471-2105-9-229","article-title":"A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences","volume":"9","author":"Chica","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012512241488400_B7","doi-asserted-by":"crossref","first-page":"2366","DOI":"10.1038\/nprot.2007.324","article-title":"Integration of biological networks and gene expression data using Cytoscape","volume":"2","author":"Cline","year":"2007","journal-title":"Nat. Protoc."},{"key":"2023012512241488400_B8","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1186\/1471-2164-6-169","article-title":"The EH1 motif in metazoan transcription factors","volume":"6","author":"Copley","year":"2005","journal-title":"BMC Genomics"},{"key":"2023012512241488400_B9","doi-asserted-by":"crossref","first-page":"W455","DOI":"10.1093\/nar\/gkm400","article-title":"The SLiMDisc server: short, linear motif discovery in proteins","volume":"35","author":"Davey","year":"2007","journal-title":"Nucleic Acids Res."},{"issue":"Suppl. 2","key":"2023012512241488400_B10","doi-asserted-by":"crossref","first-page":"W56","DOI":"10.1093\/nar\/gkr402","article-title":"SLiMSearch 2.0: biological context for short linear motifs in proteins","volume":"39","author":"Davey","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B11","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1039\/C1MB05231D","article-title":"Attributes of short linear motifs","volume":"8","author":"Davey","year":"2012","journal-title":"Mol. Biosyst."},{"key":"2023012512241488400_B12","doi-asserted-by":"crossref","first-page":"6580","DOI":"10.2741\/3175","article-title":"Understanding eukaryotic linear motifs and their role in cell signaling and regulation","volume":"13","author":"Diella","year":"2008","journal-title":"Front Biosci."},{"key":"2023012512241488400_B13","doi-asserted-by":"crossref","first-page":"D242","DOI":"10.1093\/nar\/gkr1064","article-title":"ELM\u2013the database of eukaryotic linear motifs","volume":"40","author":"Dinkel","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B14","doi-asserted-by":"crossref","first-page":"3433","DOI":"10.1093\/bioinformatics\/bti541","article-title":"IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content","volume":"21","author":"Dosztanyi","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012512241488400_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":"2023012512241488400_B16","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012512241488400_B17","doi-asserted-by":"crossref","first-page":"e967","DOI":"10.1371\/journal.pone.0000967","article-title":"SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins","volume":"2","author":"Edwards","year":"2007","journal-title":"PLoS One"},{"key":"2023012512241488400_B18","doi-asserted-by":"crossref","first-page":"2418","DOI":"10.1093\/bioinformatics\/btp424","article-title":"ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs","volume":"25","author":"Encinar","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512241488400_B19","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0506s15","article-title":"Comparative protein structure modeling using Modeller","author":"Eswar","year":"2006","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"2023012512241488400_B20","doi-asserted-by":"crossref","first-page":"D211","DOI":"10.1093\/nar\/gkp985","article-title":"The Pfam protein families database","volume":"38","author":"Finn","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B21","doi-asserted-by":"crossref","first-page":"27981","DOI":"10.1074\/jbc.M303275200","article-title":"Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-alpha","volume":"278","author":"Fontes","year":"2003","journal-title":"J. Biol. Chem."},{"key":"2023012512241488400_B22","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/nature04532","article-title":"Proteome survey reveals modularity of the yeast cell machinery","volume":"440","author":"Gavin","year":"2006","journal-title":"Nature"},{"key":"2023012512241488400_B23","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/msb.2011.18","article-title":"The multiple-specificity landscape of modular peptide recognition domains","volume":"7","author":"Gfeller","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"2023012512241488400_B24","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1038\/349132a0","article-title":"Cyclin is degraded by the ubiquitin pathway","volume":"349","author":"Glotzer","year":"1991","journal-title":"Nature"},{"key":"2023012512241488400_B25","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1074\/mcp.M700312-MCP200","article-title":"Defining the specificity space of the human SRC homology 2 domain","volume":"7","author":"Huang","year":"2008","journal-title":"Mol. Cell. Proteomics"},{"key":"2023012512241488400_B26","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1186\/1471-2105-11-507","article-title":"Proteome scanning to predict PDZ domain interactions using support vector machines","volume":"11","author":"Hui","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012512241488400_B27","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4615-0907-3","volume-title":"Learning to Classify Text Using Support Vector Machines: Methods, Theory and Algorithms.","author":"Joachims","year":"2002"},{"key":"2023012512241488400_B28","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1093\/bfgp\/eln001","article-title":"Directional and quantitative phosphorylation networks","volume":"7","author":"Jorgensen","year":"2008","journal-title":"Brief. Funct. Genomic Proteomic"},{"key":"2023012512241488400_B29","doi-asserted-by":"crossref","first-page":"4938","DOI":"10.2741\/3053","article-title":"The SH3 domain\u2013a family of versatile peptide- and protein-recognition module","volume":"13","author":"Kaneko","year":"2008","journal-title":"Front Biosci."},{"key":"2023012512241488400_B30","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1096\/fasebj.14.2.231","article-title":"The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains","volume":"14","author":"Kay","year":"2000","journal-title":"FASEB J."},{"key":"2023012512241488400_B31","doi-asserted-by":"crossref","first-page":"3437","DOI":"10.1002\/prot.22851","article-title":"Structure-based prediction of protein-peptide specificity in Rosetta","volume":"78","author":"King","year":"2010","journal-title":"Proteins"},{"key":"2023012512241488400_B32","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1478-811X-8-8","article-title":"PDZ domains and their binding partners: structure, specificity, and modification","volume":"8","author":"Lee","year":"2010","journal-title":"Cell Commun. Signal."},{"key":"2023012512241488400_B33","doi-asserted-by":"crossref","first-page":"3263","DOI":"10.1093\/nar\/gkn161","article-title":"Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach","volume":"36","author":"Li","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B34","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1042\/BJ20050411","article-title":"Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction","volume":"390","author":"Li","year":"2005","journal-title":"Biochem. J."},{"key":"2023012512241488400_B35","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1016\/j.cell.2007.05.052","article-title":"Systematic discovery of in vivo phosphorylation networks","volume":"129","author":"Linding","year":"2007","journal-title":"Cell"},{"key":"2023012512241488400_B36","doi-asserted-by":"crossref","first-page":"e1000376","DOI":"10.1371\/journal.pcbi.1000376","article-title":"Prediction of protein binding regions in disordered proteins","volume":"5","author":"Meszaros","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012512241488400_B37","doi-asserted-by":"crossref","first-page":"D252","DOI":"10.1093\/nar\/gkr1189","article-title":"Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences","volume":"40","author":"Mi","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B38","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1093\/bioinformatics\/btm624","article-title":"Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation","volume":"24","author":"Michael","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512241488400_B39","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1016\/j.jmb.2006.07.087","article-title":"Analysis of molecular recognition features (MoRFs)","volume":"362","author":"Mohan","year":"2006","journal-title":"J. Mol. Biol."},{"key":"2023012512241488400_B40","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":"2023012512241488400_B41","doi-asserted-by":"crossref","first-page":"3635","DOI":"10.1093\/nar\/gkg584","article-title":"Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs","volume":"31","author":"Obenauer","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B42","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.ceb.2007.02.013","article-title":"Dynamic control of signaling by modular adaptor proteins","volume":"19","author":"Pawson","year":"2007","journal-title":"Curr. Opin. Cell. Biol."},{"key":"2023012512241488400_B43","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/1471-2105-9-213","article-title":"A new protein linear motif benchmark for multiple sequence alignment software","volume":"9","author":"Perrodou","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012512241488400_B44","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nrm1988","article-title":"The anaphase promoting complex\/cyclosome: a machine designed to destroy","volume":"7","author":"Peters","year":"2006","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023012512241488400_B45","doi-asserted-by":"crossref","first-page":"e1000335","DOI":"10.1371\/journal.pcbi.1000335","article-title":"Accurate prediction of peptide binding sites on protein surfaces","volume":"5","author":"Petsalaki","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012512241488400_B46","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1101\/gad.14.6.655","article-title":"The KEN box: an APC recognition signal distinct from the D box targeted by Cdh1","volume":"14","author":"Pfleger","year":"2000","journal-title":"Genes Dev."},{"key":"2023012512241488400_B47","doi-asserted-by":"crossref","first-page":"21777","DOI":"10.1074\/jbc.R800084200","article-title":"Human caspases: activation, specificity, and regulation","volume":"284","author":"Pop","year":"2009","journal-title":"J. Biol. Chem."},{"key":"2023012512241488400_B48","doi-asserted-by":"crossref","first-page":"W382","DOI":"10.1093\/nar\/gki387","article-title":"The FoldX web server: an online force field","volume":"33","author":"Schymkowitz","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B49","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/j.molcel.2010.02.038","article-title":"Regulated degradation of spindle assembly factors by the anaphase-promoting complex","volume":"38","author":"Song","year":"2010","journal-title":"Mol. Cell"},{"key":"2023012512241488400_B50","doi-asserted-by":"crossref","first-page":"D698","DOI":"10.1093\/nar\/gkq1116","article-title":"The BioGRID Interaction Database: 2011 update","volume":"39","author":"Stark","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B51","doi-asserted-by":"crossref","first-page":"e1000789","DOI":"10.1371\/journal.pcbi.1000789","article-title":"Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures","volume":"6","author":"Stein","year":"2010","journal-title":"PLoS Comput. Biol."},{"key":"2023012512241488400_B52","doi-asserted-by":"crossref","first-page":"D718","DOI":"10.1093\/nar\/gkq962","article-title":"3DID: identification and classification of domain-based interactions of known three-dimensional structure","volume":"39","author":"Stein","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B53","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/j.tibs.2010.04.003","article-title":"WD40 proteins propel cellular networks","volume":"35","author":"Stirnimann","year":"2010","journal-title":"Trends Biochem. Sci."},{"key":"2023012512241488400_B54","doi-asserted-by":"crossref","first-page":"D561","DOI":"10.1093\/nar\/gkq973","article-title":"The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored","volume":"39","author":"Szklarczyk","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B55","doi-asserted-by":"crossref","first-page":"D142","DOI":"10.1093\/nar\/gkp846","article-title":"The Universal Protein Resource (UniProt) in 2010","volume":"38","author":"UniProt Consortium","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512241488400_B56","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1107\/S090744491004117X","article-title":"The Protein Data Bank in Europe (PDBe): bringing structure to biology","volume":"67","author":"Velankar","year":"2011","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"2023012512241488400_B57","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/j.molcel.2006.08.009","article-title":"A recurrent phospho-sumoyl switch in transcriptional repression and beyond","volume":"23","author":"Yang","year":"2006","journal-title":"Mol. Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/7\/976\/48881520\/bioinformatics_28_7_976.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/7\/976\/48881520\/bioinformatics_28_7_976.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:55:24Z","timestamp":1674662124000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/7\/976\/210330"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,2,10]]},"references-count":57,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2012,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts072","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,4,1]]},"published":{"date-parts":[[2012,2,10]]}}}