{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T18:27:58Z","timestamp":1725992878146},"reference-count":65,"publisher":"Elsevier","isbn-type":[{"type":"print","value":"9780128114322"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1016\/b978-0-12-809633-8.20281-1","type":"book-chapter","created":{"date-parts":[[2018,4,23]],"date-time":"2018-04-23T00:21:36Z","timestamp":1524442896000},"page":"472-487","source":"Crossref","is-referenced-by-count":0,"title":["Protein Structure Classification"],"prefix":"10.1016","author":[{"given":"Natalie L.","family":"Dawson","sequence":"first","affiliation":[]},{"given":"Sayoni","family":"Das","sequence":"additional","affiliation":[]},{"given":"Jonathan G.","family":"Lees","sequence":"additional","affiliation":[]},{"given":"Christine","family":"Orengo","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20281-1_bib1","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":"Journal of Molecular Biology"},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20281-1_bib2","doi-asserted-by":"crossref","first-page":"D310","DOI":"10.1093\/nar\/gkt1242","article-title":"SCOP2 prototype: A new approach to protein structure mining","volume":"42","author":"Andreeva","year":"2014","journal-title":"Nucleic Acids Research"},{"issue":"44","key":"10.1016\/B978-0-12-809633-8.20281-1_bib3","doi-asserted-by":"crossref","first-page":"30221","DOI":"10.1074\/jbc.R114.569350","article-title":"New insights about enzyme evolution from large scale studies of sequence and structure relationships","volume":"289","author":"Brown","year":"2014","journal-title":"The Journal of Biological Chemistry"},{"issue":"Web Server issue","key":"10.1016\/B978-0-12-809633-8.20281-1_bib4","doi-asserted-by":"crossref","first-page":"W563","DOI":"10.1093\/nar\/gkq427","article-title":"Protein annotation and modelling servers at University College London","volume":"38","author":"Buchan","year":"2010","journal-title":"Nucleic Acids Research"},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20281-1_bib5","doi-asserted-by":"crossref","first-page":"e1003926","DOI":"10.1371\/journal.pcbi.1003926","article-title":"ECOD: An evolutionary classification of protein domains","volume":"10","author":"Cheng","year":"2014","journal-title":"PLOS Computational Biology"},{"issue":"18","key":"10.1016\/B978-0-12-809633-8.20281-1_bib6","doi-asserted-by":"crossref","first-page":"2889","DOI":"10.1093\/bioinformatics\/btw473","article-title":"Functional classification of CATH superfamilies: A domain-based approach for protein function annotation","volume":"32","author":"Das","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20281-1_bib7","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.gde.2015.09.005","article-title":"Diversity in protein domain superfamilies","volume":"35","author":"Das","year":"2015","journal-title":"Current Opinion in Genetics & Development"},{"issue":"W1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib8","doi-asserted-by":"crossref","first-page":"W148","DOI":"10.1093\/nar\/gkv488","article-title":"CATH FunFHMMer web server: Protein functional annotations using functional family assignments","volume":"43","author":"Das","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib9","doi-asserted-by":"crossref","first-page":"D289","DOI":"10.1093\/nar\/gkw1098","article-title":"CATH: An expanded resource to predict protein function through structure and sequence","volume":"45","author":"Dawson","year":"2017","journal-title":"Nucleic Acids Research"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20281-1_bib10","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1016\/j.bbapap.2013.02.042","article-title":"Functional site plasticity in domain superfamilies","volume":"1834","author":"Dessailly","year":"2013","journal-title":"Biochimica Et Biophysica Acta"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20281-1_bib11","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLOS Computational Biology"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib12","doi-asserted-by":"crossref","first-page":"D190","DOI":"10.1093\/nar\/gkw1107","article-title":"InterPro in 2017-beyond protein family and domain annotations","volume":"45","author":"Finn","year":"2017","journal-title":"Nucleic Acids Research"},{"issue":"2 Pt A","key":"10.1016\/B978-0-12-809633-8.20281-1_bib13","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.jmb.2015.11.010","article-title":"Large-scale analysis exploring evolution of catalytic machineries and mechanisms in enzyme superfamilies","volume":"428","author":"Furnham","year":"2016","journal-title":"Journal of Molecular Biology"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib14","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1074\/jbc.R111.241976","article-title":"Divergence and convergence in enzyme evolution","volume":"287","author":"Galperin","year":"2012","journal-title":"The Journal of Biological Chemistry"},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20281-1_bib15","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/S1359-0278(98)00066-2","article-title":"How representative are the known structures of the proteins in a complete genome? A comprehensive structural census","volume":"3","author":"Gerstein","year":"1998","journal-title":"Folding and Design"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20281-1_bib16","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/S0959-440X(96)80058-3","article-title":"Surprising similarities in structure comparison","volume":"6","author":"Gibrat","year":"1996","journal-title":"Current Opinion in Structural Biology"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib17","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/nar\/30.1.268","article-title":"SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments","volume":"30","author":"Gough","year":"2002","journal-title":"Nucleic Acids Research"},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20281-1_bib18","doi-asserted-by":"crossref","first-page":"D291","DOI":"10.1093\/nar\/gkl959","article-title":"The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution","volume":"35","author":"Greene","year":"2007","journal-title":"Nucleic Acids Research"},{"issue":"9","key":"10.1016\/B978-0-12-809633-8.20281-1_bib19","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1016\/S0969-2126(99)80177-4","article-title":"A systematic comparison of protein structure classifications: Scop, CATH and FSSP","volume":"7","author":"Hadley","year":"1999","journal-title":"Structure"},{"issue":"W1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib20","doi-asserted-by":"crossref","first-page":"W351","DOI":"10.1093\/nar\/gkw357","article-title":"Dali server update","volume":"44","author":"Holm","year":"2016","journal-title":"Nucleic Acids Research"},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20281-1_bib21","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1093\/bioinformatics\/16.6.566","article-title":"DaliLite workbench for protein structure comparison","volume":"16","author":"Holm","year":"2000","journal-title":"Bioinformatics"},{"issue":"11","key":"10.1016\/B978-0-12-809633-8.20281-1_bib22","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1016\/S0968-0004(00)89105-7","article-title":"Dali: A network tool for protein structure comparison","volume":"20","author":"Holm","year":"1995","journal-title":"Trends in Biochemical Sciences"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20281-1_bib23","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1002\/prot.340190309","article-title":"Parser for protein folding units","volume":"19","author":"Holm","year":"1994","journal-title":"Proteins"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib24","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1093\/nar\/25.1.236","article-title":"SCOP: A Structural Classification of Proteins database","volume":"25","author":"Hubbard","year":"1997","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib25","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1186\/s13059-016-1037-6","article-title":"An expanded evaluation of protein function prediction methods shows an improvement in accuracy","volume":"17","author":"Jiang","year":"2016","journal-title":"Genome Biology"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20281-1_bib26","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1093\/bioinformatics\/14.10.846","article-title":"Hidden Markov models for detecting remote protein homologies","volume":"14","author":"Karplus","year":"1998","journal-title":"Bioinformatics"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20281-1_bib27","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nprot.2009.2","article-title":"Protein structure prediction on the Web: A case study using the Phyre server","volume":"4","author":"Kelley","year":"2009","journal-title":"Nature Protocols"},{"issue":"Pt 12 Pt 1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib28","doi-asserted-by":"crossref","first-page":"2256","DOI":"10.1107\/S0907444904026460","article-title":"Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions","volume":"60","author":"Krissinel","year":"2004","journal-title":"Acta Crystallographica Section D, Biological Crystallography"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20281-1_bib29","doi-asserted-by":"crossref","first-page":"720","DOI":"10.1093\/nar\/gkp1049","article-title":"GeMMA: Functional subfamily classification within superfamilies of predicted protein structural domains","volume":"38","author":"Lee","year":"2010","journal-title":"Nucleic Acids Research"},{"issue":"5561","key":"10.1016\/B978-0-12-809633-8.20281-1_bib30","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/261552a0","article-title":"Structural patterns in globular proteins","volume":"261","author":"Levitt","year":"1976","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20281-1_bib31","article-title":"Gene3D: Extensive prediction of globular domains in proteins","author":"Lewis","year":"2017","journal-title":"Nucleic Acids Research"},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20281-1_bib32","first-page":"D499","article-title":"Genome3D: A UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains","volume":"41","author":"Lewis","year":"2013","journal-title":"Nucleic Acids Research"},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20281-1_bib33","doi-asserted-by":"crossref","first-page":"D382","DOI":"10.1093\/nar\/gku973","article-title":"Genome3D: Exploiting structure to help users understand their sequences","volume":"43","author":"Lewis","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"14","key":"10.1016\/B978-0-12-809633-8.20281-1_bib34","doi-asserted-by":"crossref","first-page":"1761","DOI":"10.1093\/bioinformatics\/btp302","article-title":"pGenTHREADER and pDomTHREADER: New methods for improved protein fold recognition and superfamily discrimination","volume":"25","author":"Lobley","year":"2009","journal-title":"Bioinformatics"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20281-1_bib35","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1002\/prot.340230309","article-title":"Threading a database of protein cores","volume":"23","author":"Madej","year":"1995","journal-title":"Proteins"},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20281-1_bib36","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1016\/S0969-2126(98)00089-6","article-title":"Protein folds and functions","volume":"6","author":"Martin","year":"1998","journal-title":"Structure"},{"issue":"11","key":"10.1016\/B978-0-12-809633-8.20281-1_bib37","doi-asserted-by":"crossref","first-page":"2469","DOI":"10.1002\/pro.5560071126","article-title":"HOMSTRAD: A database of protein structure alignments for homologous families","volume":"7","author":"Mizuguchi","year":"1998","journal-title":"Protein Science: A Publication of the Protein Society"},{"issue":"8","key":"10.1016\/B978-0-12-809633-8.20281-1_bib38","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1016\/S0969-2126(97)00260-8","article-title":"CATH \u2013 A hierarchic classification of protein domain structures","volume":"5","author":"Orengo","year":"1997","journal-title":"Structure"},{"issue":"6507","key":"10.1016\/B978-0-12-809633-8.20281-1_bib39","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/372631a0","article-title":"Protein superfamilies and domain superfolds","volume":"372","author":"Orengo","year":"1994","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20281-1_bib40","series-title":"Protein Structure Classification","first-page":"1","author":"Pearl","year":"2015"},{"key":"10.1016\/B978-0-12-809633-8.20281-1_bib41","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/nmeth.2340","article-title":"A large-scale evaluation of computational protein function prediction","volume":"10","author":"Radivojac","year":"2013","journal-title":"Nature Methods"},{"issue":"11","key":"10.1016\/B978-0-12-809633-8.20281-1_bib42","doi-asserted-by":"crossref","first-page":"e232","DOI":"10.1371\/journal.pcbi.0030232","article-title":"CATHEDRAL: A fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures","volume":"3","author":"Redfern","year":"2007","journal-title":"PLOS Computational Biology"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20281-1_bib43","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1016\/j.jmb.2006.05.035","article-title":"Structural diversity of domain superfamilies in the CATH database","volume":"360","author":"Reeves","year":"2006","journal-title":"Journal of Molecular Biology"},{"key":"10.1016\/B978-0-12-809633-8.20281-1_bib44","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/1471-2164-11-79","article-title":"Comparative evolutionary analysis of protein complexes in E. coli and yeast","volume":"11","author":"Reid","year":"2010","journal-title":"BMC Genomics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib45","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1006\/jmbi.2001.4762","article-title":"FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties","volume":"310","author":"Shi","year":"2001","journal-title":"Journal of Molecular Biology"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib46","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1093\/nar\/29.1.228","article-title":"A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm","volume":"29","author":"Shindyalov","year":"2001","journal-title":"Nucleic Acids Research"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20281-1_bib47","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1002\/pro.5560040507","article-title":"Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions","volume":"4","author":"Siddiqui","year":"1995","journal-title":"Protein Science: A Publication of the Protein Society"},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20281-1_bib48","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1093\/bioinformatics\/bti125","article-title":"Protein homology detection by HMM-HMM comparison","volume":"21","author":"S\u00f6ding","year":"2005","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib49","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1002\/pro.5560040113","article-title":"A procedure for detecting structural domains in proteins","volume":"4","author":"Swindells","year":"1995","journal-title":"Protein Science: A Publication of the Protein Society"},{"issue":"11","key":"10.1016\/B978-0-12-809633-8.20281-1_bib50","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1002\/(SICI)1521-1878(199811)20:11<884::AID-BIES3>3.0.CO;2-H","article-title":"Contemporary approaches to protein structure classification","volume":"20","author":"Swindells","year":"1998","journal-title":"BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20281-1_bib51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0022-2836(89)90084-3","article-title":"Protein structure alignment","volume":"208","author":"Taylor","year":"1989","journal-title":"Journal of Molecular Biology"},{"issue":"25","key":"10.1016\/B978-0-12-809633-8.20281-1_bib52","doi-asserted-by":"crossref","first-page":"14658","DOI":"10.1073\/pnas.95.25.14658","article-title":"Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements","volume":"95","author":"Teichmann","year":"1998","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20281-1_bib53","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1006\/jmbi.2001.4513","article-title":"Evolution of function in protein superfamilies, from a structural perspective","volume":"307","author":"Todd","year":"2001","journal-title":"Journal of Molecular Biology"},{"key":"10.1016\/B978-0-12-809633-8.20281-1_bib54","series-title":"Proteins: Structure, Function, and Bioinformatics","article-title":"The modular structure of ThDP\u2010dependent enzymes","author":"Vogel","year":"2014"},{"issue":"suppl","key":"10.1016\/B978-0-12-809633-8.20281-1_bib55","doi-asserted-by":"crossref","first-page":"W546","DOI":"10.1093\/nar\/gkr438","article-title":"The Gene3D Web Services: A platform for identifying, annotating and comparing structural domains in protein sequences","volume":"39","author":"Yeats","year":"2011","journal-title":"Nucleic Acids Research"},{"year":"1999","series-title":"Introduction to Protein Structure","author":"Branden","key":"10.1016\/B978-0-12-809633-8.20281-1_fur1"},{"key":"10.1016\/B978-0-12-809633-8.20281-1_fur2","series-title":"Protein Bioinformatics: From Protein Modifications and Networks to Proteomics","first-page":"79","article-title":"CATH-Gene3D: Generation of the Resource and its use in Obtaining Structural and Functional Annotations for Protein Sequences","author":"Dawson","year":"2017"},{"year":"2009","series-title":"Structural Bioinformatics","key":"10.1016\/B978-0-12-809633-8.20281-1_fur3"},{"year":"2010","series-title":"Introduction to Protein Science: Architecture, Function and Genomics","author":"Lesk","key":"10.1016\/B978-0-12-809633-8.20281-1_fur4"},{"year":"2004","series-title":"Bioinformatics: Sequence and Genome Analysis","author":"Mount","key":"10.1016\/B978-0-12-809633-8.20281-1_fur5"},{"key":"10.1016\/B978-0-12-809633-8.20281-1_fur6","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nbt.3886","article-title":"1003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life","volume":"35","author":"Mukherjee","year":"2017","journal-title":"Nature Biotechnology"},{"year":"2013","series-title":"Protein Families: Relating Protein Sequence, Structure, and Function","key":"10.1016\/B978-0-12-809633-8.20281-1_fur7"},{"year":"2003","series-title":"Bioinformatics: Genes, Proteins and Computers","key":"10.1016\/B978-0-12-809633-8.20281-1_fur8"},{"key":"10.1016\/B978-0-12-809633-8.20281-1_fur9","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nature24286","article-title":"DNA sequencing at 40: Past, present and future","volume":"550","author":"Shendure","year":"2017","journal-title":"Nature"},{"year":"2012","series-title":"How Proteins Work","author":"Williamson","key":"10.1016\/B978-0-12-809633-8.20281-1_fur10"}],"container-title":["Encyclopedia of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338202811?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338202811?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T19:29:09Z","timestamp":1548098949000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/B9780128096338202811"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9780128114322"],"references-count":65,"URL":"https:\/\/doi.org\/10.1016\/b978-0-12-809633-8.20281-1","relation":{},"subject":[],"published":{"date-parts":[[2019]]}}}