{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T11:23:04Z","timestamp":1768562584637,"version":"3.49.0"},"reference-count":17,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2022,4,12]],"date-time":"2022-04-12T00:00:00Z","timestamp":1649721600000},"content-version":"vor","delay-in-days":101,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board","doi-asserted-by":"publisher","award":["R. Sowdhamini's JC Bose Fellowship (SB\/S2\/JC-071\/2"],"award-info":[{"award-number":["R. Sowdhamini's JC Bose Fellowship (SB\/S2\/JC-071\/2"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["R. Sowdhamini's Bioinformatics Centre Grant (BT\/PR"],"award-info":[{"award-number":["R. Sowdhamini's Bioinformatics Centre Grant (BT\/PR"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001412","name":"Council of Scientific and Industrial Research, India","doi-asserted-by":"publisher","award":["Vasundhara Gadiyaram's CSIR-RA fellowship"],"award-info":[{"award-number":["Vasundhara Gadiyaram's CSIR-RA fellowship"]}],"id":[{"id":"10.13039\/501100001412","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:label\/>\n                  <jats:p>Sequence alignments are models that capture the structural, functional and evolutionary relationships between proteins. Structure-guided sequence alignments are helpful in the case of distantly related proteins with poor sequence identity, thus rendering routine sequence alignment methods ineffective. Protein Alignment organized as Structural Superfamilies or PASS2 database provides such sequence alignments of protein domains within a superfamily as per the Structural Classification of Proteins extended (SCOPe) database. The current update of PASS2 (i.e. PASS2.7) is following the latest release of SCOPe (2.07) and we provide data for 14\u2009323 protein domains that are &amp;lt;40% identical and are organized into 2024 superfamilies. Several useful features derived from the alignments, such as conserved secondary structural motifs, HMMs and residues conserved across the superfamily, are also reported. Protein domains that are deviant from the rest of the members of a superfamily may compromise the quality of the alignment, and we found this to be the case in \u223c7% of the total superfamilies we considered. To improve the alignment by objectively identifying such \u2018outliers\u2019, in this update, we have used a k-means-based unsupervised machine learning method for clustering superfamily members, where features provided were length of domains aligned, C\u03b1-RMSD derived from the rigid-body superposition of all members and gaps contributed to the alignment by each domain. In a few cases, we have split the superfamily as per the clusters predicted and provided complete data for each cluster. A new feature included in this update is absolutely conserved interactions (ACIs) between residue backbones and side chains, which are obtained by aligning protein structure networks using structure-guided sequence alignments of superfamilies. ACIs provide valuable information about functionally important residues and the structure\u2013function relationships of proteins. The ACIs and the corresponding conserved networks for backbone and sidechain have been marked on the superimposed structure separately.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Database URL<\/jats:title>\n                  <jats:p>The updated version of the PASS2 database is available at http:\/\/caps.ncbs.res.in\/pass2\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/database\/baac025","type":"journal-article","created":{"date-parts":[[2022,3,27]],"date-time":"2022-03-27T19:06:37Z","timestamp":1648407997000},"source":"Crossref","is-referenced-by-count":6,"title":["PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe"],"prefix":"10.1093","volume":"2022","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9336-2796","authenticated-orcid":false,"given":"Teerna","family":"Bhattacharyya","sequence":"first","affiliation":[{"name":"National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, Karnataka 560065, India"}]},{"given":"Soumya","family":"Nayak","sequence":"additional","affiliation":[{"name":"National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, Karnataka 560065, India"}]},{"given":"Smit","family":"Goswami","sequence":"additional","affiliation":[{"name":"National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, Karnataka 560065, India"}]},{"given":"Vasundhara","family":"Gadiyaram","sequence":"additional","affiliation":[{"name":"National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, Karnataka 560065, India"}]},{"given":"Oommen K","family":"Mathew","sequence":"additional","affiliation":[{"name":"National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, Karnataka 560065, 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 (TIFR), Bellary Road, Bangalore, Karnataka 560065, India"}]}],"member":"286","published-online":{"date-parts":[[2022,4,12]]},"reference":[{"key":"2022041207473863700_R1","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":"2022041207473863700_R2","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":"2022041207473863700_R3","doi-asserted-by":"crossref","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 Bioinform."},{"key":"2022041207473863700_R4","doi-asserted-by":"crossref","first-page":"53","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":"2022041207473863700_R5","doi-asserted-by":"publisher","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":"2022041207473863700_R6","doi-asserted-by":"publisher","first-page":"baz028, 1","DOI":"10.1093\/database\/baz028","article-title":"PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe","volume":"2019","author":"Ghosh","year":"2019","journal-title":"Database"},{"key":"2022041207473863700_R7","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":"2022041207473863700_R8","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":"2022041207473863700_R9","doi-asserted-by":"crossref","first-page":"0088","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. 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