{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T17:39:36Z","timestamp":1773423576864,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2017,5,12]],"date-time":"2017-05-12T00:00:00Z","timestamp":1494547200000},"content-version":"vor","delay-in-days":1989,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1]]},"DOI":"10.1093\/nar\/gkr1129","type":"journal-article","created":{"date-parts":[[2011,12,3]],"date-time":"2011-12-03T05:55:26Z","timestamp":1322891726000},"page":"D490-D494","source":"Crossref","is-referenced-by-count":4,"title":["Cube-DB: detection of functional divergence in human protein families"],"prefix":"10.1093","volume":"40","author":[{"given":"Zong Hong","family":"Zhang","sequence":"first","affiliation":[]},{"given":"Kavitha","family":"Bharatham","sequence":"additional","affiliation":[]},{"given":"Sharon M. Q.","family":"Chee","sequence":"additional","affiliation":[]},{"given":"Ivana","family":"Mihalek","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2011,12,1]]},"reference":[{"key":"key\n\t\t\t\t20170512123919_gkr1129-B1","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1093\/oxfordjournals.molbev.a003824","article-title":"Maximum-likelihood approach for gene family evolution under functional divergence","volume":"18","author":"Gu","year":"2001","journal-title":"Mol. Biol. Evol"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/oxfordjournals.molbev.a003973","article-title":"Heterotachy, an important process of protein evolution","volume":"19","author":"Lopez","year":"2002","journal-title":"Mol. Biol. Evol"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B3","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1093\/bioinformatics\/btn214","article-title":"Characterization and prediction of residues determining protein functional specificity","volume":"24","author":"Capra","year":"2008","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B4","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1006\/jmbi.1997.1395","article-title":"Identification of functional surfaces of the zinc binding domains of intracellular receptors1","volume":"274","author":"Lichtarge","year":"1997","journal-title":"J. Mol. Biol"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B5","doi-asserted-by":"crossref","first-page":"8126","DOI":"10.1074\/jbc.M312671200","article-title":"Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions","volume":"279","author":"Madabushi","year":"2004","journal-title":"J. Biol. Chem"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B6","doi-asserted-by":"crossref","first-page":"D197","DOI":"10.1093\/nar\/gki067","article-title":"FunShift: a database of function shift analysis on protein subfamilies","volume":"33","author":"Abhiman","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B7","doi-asserted-by":"crossref","first-page":"14512","DOI":"10.1073\/pnas.251526398","article-title":"A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins","volume":"98","author":"Knudsen","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B8","doi-asserted-by":"crossref","first-page":"D191","DOI":"10.1093\/nar\/gkn716","article-title":"SDR: a database of predicted specificity-determining residues in proteins","volume":"37","author":"Donald","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B9","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1186\/1471-2105-10-207","article-title":"Ensemble approach to predict specificity determinants: benchmarking and validation","volume":"10","author":"Chakrabarti","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B10","doi-asserted-by":"crossref","first-page":"1995","DOI":"10.1073\/pnas.0908044107","article-title":"Protein interactions and ligand binding: from protein subfamilies to functional specificity","volume":"107","author":"Rausell","year":"2010","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B11","doi-asserted-by":"crossref","first-page":"e24382","DOI":"10.1371\/journal.pone.0024382","article-title":"Determinants, discriminants, conserved residues - a heuristic approach to detection of functional divergence in protein families","volume":"6","author":"Bharatham","year":"2011","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B12","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1110\/ps.03191704","article-title":"Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families","volume":"13","author":"Kalinina","year":"2004","journal-title":"Protein Sci"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B13","doi-asserted-by":"crossref","first-page":"W110","DOI":"10.1093\/nar\/gkl203","article-title":"TreeDet: a web server to explore sequence space","volume":"34","author":"Carro","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B14","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1016\/j.jmb.2007.08.036","article-title":"Functional specificity lies within the properties and evolutionary changes of amino acids","volume":"373","author":"Chakrabarti","year":"2007","journal-title":"J. Mol. Biol"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B15","doi-asserted-by":"crossref","first-page":"D514","DOI":"10.1093\/nar\/gkq892","article-title":"genenames. org: the HGNC resources in 2011","volume":"39","author":"Seal","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B16","doi-asserted-by":"crossref","first-page":"D800","DOI":"10.1093\/nar\/gkq1064","article-title":"Ensembl 2011","volume":"39","author":"Flicek","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B17","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1126\/science.278.5338.631","article-title":"A genomic perspective on protein families","volume":"278","author":"Tatusov","year":"1997","journal-title":"Science"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B18","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1073\/pnas.96.6.2896","article-title":"The use of gene clusters to infer functional coupling","volume":"96","author":"Overbeek","year":"1999","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B19","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1093\/protein\/12.2.85","article-title":"Twilight zone of protein sequence alignments","volume":"12","author":"Rost","year":"1999","journal-title":"Protein Eng"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B20","doi-asserted-by":"crossref","first-page":"e1000262","DOI":"10.1371\/journal.pcbi.1000262","article-title":"Phylogenetic and functional assessment of orthologs inference projects and methods","volume":"5","author":"Altenhoff","year":"2009","journal-title":"PLoS Comput. Biol"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B21","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/nar\/gki198","article-title":"MAFFT version 5: improvement in accuracy of multiple sequence alignment","volume":"33","author":"Katoh","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B22"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B23","author":"DeLano","journal-title":"The PyMOL Molecular Graphics System."},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B24","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B25","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1006\/jmbi.1999.3230","article-title":"Mutational and structural analysis of the binding interface between type I interferons and their receptor ifnar2","volume":"294","author":"Piehler","year":"1999","journal-title":"J. Mol. Biol"},{"key":"key\n\t\t\t\t20170512123919_gkr1129-B26","doi-asserted-by":"crossref","first-page":"14755","DOI":"10.1021\/ja205480v","article-title":"Observation of intermolecular interactions in large protein complexes by 2D-double difference NOESY: application to the 44\u2009kDa interferon-receptor complex","volume":"133","author":"Nudelman","year":"2011","journal-title":"J. Am. Chem. Soc"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T14:42:03Z","timestamp":1522680123000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gkr1129"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,12,1]]},"references-count":26,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2011,12,1]]},"published-print":{"date-parts":[[2012,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkr1129","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published":{"date-parts":[[2011,12,1]]}}}