{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T12:34:48Z","timestamp":1763037288161,"version":"3.37.3"},"reference-count":27,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,3,1]],"date-time":"2019-03-01T00:00:00Z","timestamp":1551398400000},"content-version":"vor","delay-in-days":59,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology","doi-asserted-by":"publisher","award":["BT\/01\/COE\/09\/01"],"award-info":[{"award-number":["BT\/01\/COE\/09\/01"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board","doi-asserted-by":"publisher","award":["SB\/S2\/JCB-071\/2015"],"award-info":[{"award-number":["SB\/S2\/JCB-071\/2015"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"DOI":"10.1093\/database\/baz028","type":"journal-article","created":{"date-parts":[[2019,2,26]],"date-time":"2019-02-26T19:30:03Z","timestamp":1551209403000},"source":"Crossref","is-referenced-by-count":2,"title":["PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe"],"prefix":"10.1093","volume":"2019","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3641-6393","authenticated-orcid":false,"given":"Pritha","family":"Ghosh","sequence":"first","affiliation":[{"name":"National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9336-2796","authenticated-orcid":false,"given":"Teerna","family":"Bhattacharyya","sequence":"additional","affiliation":[{"name":"National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6312-3118","authenticated-orcid":false,"given":"Oommen K","family":"Mathew","sequence":"additional","affiliation":[{"name":"National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6642-2367","authenticated-orcid":false,"given":"Ramanathan","family":"Sowdhamini","sequence":"additional","affiliation":[{"name":"National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, India"}]}],"member":"286","published-online":{"date-parts":[[2019,3,1]]},"reference":[{"key":"key\n\t\t\t\t2019030101303739400_ref1","doi-asserted-by":"crossref","first-page":"D304","DOI":"10.1093\/nar\/gkt1240","article-title":"SCOPe: Structural Classification of Proteins\u2014extended, integrating SCOP and ASTRAL data and classification of new structures","volume":"42","author":"Fox","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019030101303739400_ref2","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1093\/nar\/30.1.284","article-title":"PASS2: a semi-automated database of protein alignments organised as structural superfamilies","volume":"30","author":"Mallika","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019030101303739400_ref3","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/1471-2105-5-35","article-title":"PASS2: an automated database of protein alignments organised as structural superfamilies","volume":"5","author":"Bhaduri","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t2019030101303739400_ref4","doi-asserted-by":"crossref","first-page":"D410","DOI":"10.1093\/nar\/gkv1205","article-title":"PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features","volume":"44","author":"Gandhimathi","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019030101303739400_ref5","doi-asserted-by":"crossref","first-page":"e10","DOI":"10.1371\/journal.pcbi.0040010","article-title":"Matt: local flexibility aids protein multiple structure alignment","volume":"4","author":"Menke","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t2019030101303739400_ref6","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1093\/bioinformatics\/14.7.617","article-title":"JOY: protein sequence-structure representation and analysis","volume":"14","author":"Mizuguchi","year":"1998","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019030101303739400_ref7","first-page":"403","article-title":"Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming","volume":"212","author":"\u0160ali","year":"1990","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t2019030101303739400_ref8","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1093\/protein\/1.5.377","article-title":"Knowledge based modelling of homologous proteins, part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures","volume":"1","author":"Sutcliffe","year":"1987","journal-title":"Protein Eng."},{"key":"key\n\t\t\t\t2019030101303739400_ref9","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1107\/S0567739472001627","article-title":"A mathematical procedure for superimposing atomic coordinates of proteins","volume":"28","author":"McLachlan","year":"1972","journal-title":"Acta Crystallogr. A"},{"key":"key\n\t\t\t\t2019030101303739400_ref10","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.febslet.2004.05.028","article-title":"Regions of minimal structural variation among members of protein domain superfamilies: application to remote homology detection and modelling using distant relationships","volume":"569","author":"Chakrabarti","year":"2004","journal-title":"FEBS Lett."},{"key":"key\n\t\t\t\t2019030101303739400_ref11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0074416","article-title":"Rebelling for a reason: protein structural \u201coutliers\u201d","volume":"8","author":"Arumugam","year":"2013","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t2019030101303739400_ref12","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":"key\n\t\t\t\t2019030101303739400_ref13","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1073\/pnas.91.3.1059","article-title":"Hidden Markov models of biological primary sequence information","volume":"91","author":"Baldi","year":"1994","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"key\n\t\t\t\t2019030101303739400_ref14","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1093\/bioinformatics\/btl679","article-title":"SMotif: a server for structural motifs in proteins","volume":"23","author":"Pugalenthi","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019030101303739400_ref15","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/1472-6807-8-28","article-title":"CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations","volume":"8","author":"Sandhya","year":"2008","journal-title":"BMC Struct. Biol."},{"key":"key\n\t\t\t\t2019030101303739400_ref16","doi-asserted-by":"crossref","first-page":"D530","DOI":"10.1093\/nar\/gks1050","article-title":"Gene ontology annotations and resources","volume":"41","author":"Consortium","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019030101303739400_ref17","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019030101303739400_ref18","doi-asserted-by":"crossref","first-page":"e12267","DOI":"10.1371\/journal.pone.0012267","article-title":"jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web","volume":"5","author":"Smits","year":"2010","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t2019030101303739400_ref19","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: a structural classification of proteins database for the investigation of sequences and structures","volume":"247","author":"Murzin","year":"1995","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t2019030101303739400_ref20","doi-asserted-by":"crossref","first-page":"13576","DOI":"10.1074\/jbc.M414508200","article-title":"Crystal structure of vinorine synthase, the first representative of the BAHD superfamily","volume":"280","author":"Ma","year":"2005","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t2019030101303739400_ref21","first-page":"307","article-title":"Sequence and structural analyses of Interleukin-8-like chemokine superfamily","volume":"8","author":"Kanagarajadurai","year":"2008","journal-title":"In Silico Biol."},{"key":"key\n\t\t\t\t2019030101303739400_ref22","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1172\/JCI114265","article-title":"Neutrophil-activating peptide-1\/interleukin 8, a novel cytokine that activates neutrophils","volume":"84","author":"Baggiolini","year":"1989","journal-title":"J. Clin. Invest."},{"key":"key\n\t\t\t\t2019030101303739400_ref23","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1186\/1471-2105-8-355","article-title":"Accuracy of structure-based sequence alignment of automatic methods","volume":"8","author":"Kim","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t2019030101303739400_ref24","doi-asserted-by":"crossref","first-page":"14","DOI":"10.4018\/jkdb.2011100104","article-title":"PASS2: a database of structure-based sequence alignments of protein structural domain superfamilies","volume":"2","author":"Kanagarajadurai","year":"2011","journal-title":"Int. J. Knowl. Discov. Bioinform."},{"key":"key\n\t\t\t\t2019030101303739400_ref25","doi-asserted-by":"crossref","first-page":"D531","DOI":"10.1093\/nar\/gkr1096","article-title":"PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies","volume":"40","author":"Gandhimathi","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019030101303739400_ref26","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1186\/s12859-016-1289-x","article-title":"RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information","volume":"17","author":"Ghosh","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t2019030101303739400_ref27","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1002\/prot.21741","article-title":"Evolution of binding sites for zinc and calcium ions playing structural roles","volume":"71","author":"Torrance","year":"2008","journal-title":"Proteins"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baz028\/27996496\/baz028.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,3,1]],"date-time":"2019-03-01T01:31:09Z","timestamp":1551403869000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baz028\/5367127"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,1]]},"references-count":27,"URL":"https:\/\/doi.org\/10.1093\/database\/baz028","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2019]]},"published":{"date-parts":[[2019,1,1]]}}}