{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,26]],"date-time":"2026-04-26T06:20:31Z","timestamp":1777184431843,"version":"3.51.4"},"reference-count":29,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,2,26]],"date-time":"2019-02-26T00:00:00Z","timestamp":1551139200000},"content-version":"vor","delay-in-days":56,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P20GM103446"],"award-info":[{"award-number":["P20GM103446"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U24HG007822"],"award-info":[{"award-number":["U24HG007822"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"institutional resources of the Center for Bioinformatics and Computational Biology"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"DOI":"10.1093\/database\/baz026","type":"journal-article","created":{"date-parts":[[2019,2,5]],"date-time":"2019-02-05T15:19:57Z","timestamp":1549379997000},"source":"Crossref","is-referenced-by-count":7,"title":["PIRSitePredict for protein functional site prediction using position-specific rules"],"prefix":"10.1093","volume":"2019","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7287-9013","authenticated-orcid":false,"given":"Chuming","family":"Chen","sequence":"first","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA"},{"name":"Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinghua","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA"},{"name":"Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongzhan","family":"Huang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA"},{"name":"Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cholanayakanahalli R","family":"Vinayaka","sequence":"additional","affiliation":[{"name":"Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John S","family":"Garavelli","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cecilia N","family":"Arighi","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA"},{"name":"Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Darren A","family":"Natale","sequence":"additional","affiliation":[{"name":"Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cathy H","family":"Wu","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA"},{"name":"Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA"},{"name":"Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,2,26]]},"reference":[{"key":"key\n\t\t\t\t2019022601503126000_ref1","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1186\/gb-2009-10-2-206","article-title":"Sequence-based feature prediction and annotation of proteins","volume":"10","author":"Juncker","year":"2009","journal-title":"Genome Biol. (Online Edition)"},{"key":"key\n\t\t\t\t2019022601503126000_ref2","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1038\/nrg1113","article-title":"Classification schemes for protein structure and function","volume":"4","author":"Ouzounis","year":"2003","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t2019022601503126000_ref3","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1093\/bioinformatics\/btg036","article-title":"Prediction of human protein function according to Gene Ontology categories","volume":"19","author":"Jensen","year":"2003","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019022601503126000_ref4","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1038\/nprot.2013.092","article-title":"Large-scale gene function analysis with the PANTHER classification system","volume":"8","author":"Mi","year":"2013","journal-title":"Nat. Protoc."},{"key":"key\n\t\t\t\t2019022601503126000_ref5","doi-asserted-by":"crossref","first-page":"D260","DOI":"10.1093\/nar\/gkl1043","article-title":"TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes","volume":"35","author":"Selengut","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref6","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 Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref7","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 Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref8","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.ymeth.2015.09.029","article-title":"Protein function annotation using protein domain family resources","volume":"93","author":"Das","year":"2016","journal-title":"Methods"},{"key":"key\n\t\t\t\t2019022601503126000_ref9","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 Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref10","doi-asserted-by":"crossref","first-page":"W573","DOI":"10.1093\/nar\/gkm297","article-title":"Firestar\u2014prediction of functionally important residues using structural templates and alignment reliability","volume":"35","author":"L\u00f3pez","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref11","doi-asserted-by":"crossref","first-page":"D294","DOI":"10.1093\/nar\/gkv1291","article-title":"ELM 2016\u2014data update and new functionality of the eukaryotic linear motif resource","volume":"44","author":"Dinkel","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref12","first-page":"184","volume-title":"Handbook of Research on Computational Intelligence Applications in Bioinformatics","author":"Sneha","year":"2016"},{"key":"key\n\t\t\t\t2019022601503126000_ref13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.5936\/csbj.201308005","article-title":"Structure-based methods for computational protein functional site prediction","volume":"8","author":"Dukka","year":"2013","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"key\n\t\t\t\t2019022601503126000_ref14","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1070\/RC2014v083n02ABEH004377","article-title":"Prediction of protein post-translational modifications: main trends and methods","volume":"83","author":"Sobolev","year":"2014","journal-title":"Russ. Chem. Rev."},{"key":"key\n\t\t\t\t2019022601503126000_ref15","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1002\/pmic.200300771","article-title":"Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence","volume":"4","author":"Blom","year":"2004","journal-title":"Proteomics"},{"key":"key\n\t\t\t\t2019022601503126000_ref16","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.csbj.2017.03.004","article-title":"Protein post-translational modifications: in silico prediction tools and molecular modeling","volume":"15","author":"Audagnotto","year":"2017","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"key\n\t\t\t\t2019022601503126000_ref17","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1007\/978-1-61779-176-5_20","volume-title":"In Silico Tools for Gene Discovery","author":"Liu","year":"2011"},{"key":"key\n\t\t\t\t2019022601503126000_ref18","doi-asserted-by":"crossref","first-page":"D261","DOI":"10.1093\/nar\/gkq1104","article-title":"Phospho.ELM: a database of phosphorylation sites\u2014update 2011","volume":"39","author":"Dinkel","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref19","doi-asserted-by":"crossref","first-page":"D618","DOI":"10.1093\/nar\/gkx1012","article-title":"Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites","volume":"46","author":"Ribeiro","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref20","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1007\/978-1-60327-241-4_21","article-title":"Prediction of posttranslational modification of proteins from their amino acid sequence","volume":"609","author":"Eisenhaber","year":"2010","journal-title":"Methods Mol. Biol."},{"key":"key\n\t\t\t\t2019022601503126000_ref21","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/978-1-60761-977-2_7","article-title":"Structure-guided rule-based annotation of protein functional sites in UniProt Knowledgebase","volume":"694","author":"Vasudevan","year":"2011","journal-title":"Methods Mol. Biol."},{"key":"key\n\t\t\t\t2019022601503126000_ref22","first-page":"197","article-title":"PIRSF family classification system for protein functional and evolutionary analysis","volume":"2","author":"Nikolskaya","year":"2007","journal-title":"Evol. Bioinform. Online"},{"key":"key\n\t\t\t\t2019022601503126000_ref23","doi-asserted-by":"crossref","first-page":"D190","DOI":"10.1093\/nar\/gkw1107","article-title":"InterPro in 2017\u2014beyond protein family and domain annotations","volume":"45","author":"Finn","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref24","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"The UniProt Consortium","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref25","doi-asserted-by":"crossref","first-page":"e121","DOI":"10.1093\/nar\/gkt263","article-title":"Challenges in Homology Search: HMMER3 and convergent evolution of coiled-coil regions","volume":"41","author":"Mistry","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref26","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Trinity: reconstructing a full-length transcriptome without a genome from RNA-seq data","volume":"29","author":"Manfred","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t2019022601503126000_ref27","doi-asserted-by":"crossref","first-page":"191","DOI":"10.12688\/f1000research.4996.1","article-title":"SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes","volume":"3","author":"Wyffels","year":"2014","journal-title":"F1000Res"},{"key":"key\n\t\t\t\t2019022601503126000_ref28","doi-asserted-by":"crossref","first-page":"D1064","DOI":"10.1093\/nar\/gku1002","article-title":"HAMAP in 2015: updates to the protein family classification and annotation system","volume":"43","author":"Pedruzzi","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019022601503126000_ref29","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1186\/s13104-016-1927-4","article-title":"Seqotron: a user-friendly sequence editor for Mac OS X","volume":"9","author":"Fourment","year":"2016","journal-title":"BMC. Res. Notes"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baz026\/27977606\/baz026.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,2,26]],"date-time":"2019-02-26T01:51:04Z","timestamp":1551145864000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baz026\/5363830"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,1]]},"references-count":29,"URL":"https:\/\/doi.org\/10.1093\/database\/baz026","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019]]},"published":{"date-parts":[[2019,1,1]]}}}