{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,15]],"date-time":"2024-09-15T16:11:40Z","timestamp":1726416700666},"reference-count":29,"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\/b978-0-12-809633-8.12364-7","type":"book-chapter","created":{"date-parts":[[2017,8,11]],"date-time":"2017-08-11T23:48:23Z","timestamp":1502495303000},"page":"8-14","source":"Crossref","is-referenced-by-count":0,"title":["Protein Functional Annotation"],"prefix":"10.1016","author":[{"given":"Pier","family":"Luigi Martelli","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giuseppe","family":"Profiti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rita","family":"Casadio","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib1","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bas019","article-title":"The PRINTS database: A fine-grained protein sequence annotation and analysis resource \u2013 Its status in 2012","volume":"2012","author":"Attwood","year":"2012","journal-title":"Database"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib2","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1002\/j.1460-2075.1986.tb04288.x","article-title":"The relation between the divergence of sequence and structure in proteins","volume":"5","author":"Chothia","year":"1986","journal-title":"EMBO Journal"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib3","doi-asserted-by":"crossref","first-page":"S14","DOI":"10.1186\/1471-2105-13-S4-S14","article-title":"Argot2: A large scale function prediction tool relying on semantic similarity of weighted gene ontology terms","volume":"13","author":"Falda","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib4","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: Towards a more sustainable future","volume":"44","author":"Finn","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib5","doi-asserted-by":"crossref","first-page":"D485","DOI":"10.1093\/nar\/gkt1243","article-title":"The catalytic site atlas 2.0: Cataloging catalytic sites and residues identified in enzymes","volume":"42","author":"Furnham","year":"2014","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib6","doi-asserted-by":"crossref","first-page":"D261","DOI":"10.1093\/nar\/gku1223","article-title":"Expanded microbial genome coverage and improved protein family annotation in the COG database","volume":"43","author":"Galperin","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib7","doi-asserted-by":"crossref","first-page":"3420","DOI":"10.1093\/nar\/gkn176","article-title":"High-throughput functional annotation and data mining with the Blast2GO suite","volume":"36","author":"G\u00f6tz","year":"2008","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib8","doi-asserted-by":"crossref","first-page":"W545","DOI":"10.1093\/nar\/gkq366","article-title":"Dali server: Conservation mapping in 3D","volume":"38","author":"Holm","year":"2010","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib9","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1472-6807-6-19","article-title":"LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation","volume":"6","author":"Huang","year":"2006","journal-title":"BMC Structural Biology"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib10","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"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib11","doi-asserted-by":"crossref","first-page":"2308","DOI":"10.1021\/acs.jcim.5b00534","article-title":"ProBiS-CHARMMing: Web interface for prediction and optimization of ligands in protein binding sites","volume":"55","author":"Konc","year":"2015","journal-title":"Journal of Chemical Information and Modeling"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib12","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 D"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib13","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkr825","article-title":"Pocketome: An encyclopedia of small-molecule binding sites in 4D","volume":"40","author":"Kufareva","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib14","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1186\/1471-2105-14-S3-S8","article-title":"MS-kNN: Protein function prediction by integrating multiple data sources","volume":"14","author":"Lan","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib15","doi-asserted-by":"crossref","first-page":"W89","DOI":"10.1093\/nar\/gki414","article-title":"ProFunc: A server for predicting protein function from 3D structure","volume":"33","author":"Laskowski","year":"2005","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib16","doi-asserted-by":"crossref","first-page":"D257","DOI":"10.1093\/nar\/gku949","article-title":"SMART: Recent updates, new developments and status in 2015","volume":"43","author":"Letunic","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib17","doi-asserted-by":"crossref","first-page":"D297","DOI":"10.1093\/nar\/gkt1208","article-title":"MMDB and VAST+: Tracking structural similarities between macromolecular complexes","volume":"42","author":"Madej","year":"2014","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib18","doi-asserted-by":"crossref","first-page":"D200","DOI":"10.1093\/nar\/gkw1129","article-title":"CDD\/SPARCLE: Functional classification of proteins via subfamily domain architectures","volume":"45","author":"Marchler-Bauer","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib19","doi-asserted-by":"crossref","first-page":"e63754","DOI":"10.1371\/journal.pone.0063754","article-title":"FFPred 2.0: Improved homology-independent prediction of gene ontology terms for eukaryotic protein sequences","volume":"8","author":"Minneci","year":"2013","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib20","doi-asserted-by":"crossref","first-page":"W134","DOI":"10.1093\/nar\/gkv523","article-title":"INGA: Protein function prediction combining interaction networks, domain assignments and sequence similarity","volume":"43","author":"Piovesan","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib21","doi-asserted-by":"crossref","first-page":"W285","DOI":"10.1093\/nar\/gkx330","article-title":"The Bologna Annotation Resource (BAR 3.0): Improving protein functional annotation","volume":"45","author":"Profiti","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib29","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/S0022-2836(02)00016-5","article-title":"Enzyme function less conserved than anticipated","volume":"318","author":"Rost","year":"2002","journal-title":"Journal of Molecular Biology"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib22","doi-asserted-by":"crossref","first-page":"W141","DOI":"10.1093\/nar\/gkv461","article-title":"SIFTER search: A web server for accurate phylogeny-based protein function prediction","volume":"43","author":"Sahraeian","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib23","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"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib24","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gks1067","article-title":"New and continuing developments at PROSITE","volume":"41","author":"Sigrist","year":"2013","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib25","doi-asserted-by":"crossref","first-page":"D490","DOI":"10.1093\/nar\/gks1211","article-title":"New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures","volume":"41","author":"Sillitoe","year":"2013","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib26","doi-asserted-by":"crossref","first-page":"D376","DOI":"10.1093\/nar\/gku947","article-title":"CATH: Comprehensive structural and functional annotations for genome sequences","volume":"43","author":"Sillitoe","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib27","doi-asserted-by":"crossref","first-page":"582765","DOI":"10.1155\/2012\/582765","article-title":"Exploring biomolecular literature with EVEX: Connecting genes through events, homology, and indirect associations","volume":"2012","author":"Van Landeghem","year":"2012","journal-title":"Advanced Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.12364-7_bib28","doi-asserted-by":"crossref","first-page":"W466","DOI":"10.1093\/nar\/gks489","article-title":"CombFunc: Predicting protein function using heterogeneous data sources","volume":"40","author":"Wass","year":"2012","journal-title":"Nucleic Acids Research"}],"container-title":["Encyclopedia of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338123647?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338123647?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2020,10,15]],"date-time":"2020-10-15T02:54:55Z","timestamp":1602730495000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/B9780128096338123647"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9780128114322"],"references-count":29,"URL":"https:\/\/doi.org\/10.1016\/b978-0-12-809633-8.12364-7","relation":{},"subject":[],"published":{"date-parts":[[2019]]}}}