{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,3,30]],"date-time":"2022-03-30T09:29:36Z","timestamp":1648632576744},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2013,11,15]],"date-time":"2013-11-15T00:00:00Z","timestamp":1384473600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BioData Mining"],"published-print":{"date-parts":[[2013,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Influx of newly determined crystal structures into primary structural databases is increasing at a rapid pace. This leads to updation of primary and their dependent secondary databases which makes large scale analysis of structures even more challenging. Hence, it becomes essential to compare and appreciate replacement of data and inclusion of new data that is critical between two updates. PASS2 is a database that retains structure-based sequence alignments of protein domain superfamilies and relies on SCOP database for its hierarchy and definition of superfamily members. Since, accurate alignments of distantly related proteins are useful evolutionary models for depicting variations within protein superfamilies, this study aims to trace the changes in data in between PASS2 updates.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this study, differences in superfamily compositions, family constituents and length variations between different versions of PASS2 have been tracked. Studying length variations in protein domains, which have been introduced by indels (insertions\/deletions), are important because theses indels act as evolutionary signatures in introducing variations in substrate specificity, domain interactions and sometimes even regulating protein stability. With this objective of classifying the nature and source of variations in the superfamilies during transitions (between the different versions of PASS2), increasing length-rigidity of the superfamilies in the recent version is observed. In order to study such length-variant superfamilies in detail, an improved classification approach is also presented, which divides the superfamilies into distinct groups based on their extent of length variation.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>An objective study in terms of transition between the database updates, detailed investigation of the new\/old members and examination of their structural alignments is non-trivial and will help researchers in designing experiments on specific superfamilies, in various modelling studies, in linking representative superfamily members to rapidly expanding sequence space and in evaluating the effects of length variations of new members in drug target proteins. The improved objective classification scheme developed here would be useful in future for automatic analysis of length variation in cases of updates of databases or even within different secondary databases.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1756-0381-6-20","type":"journal-article","created":{"date-parts":[[2013,11,15]],"date-time":"2013-11-15T19:02:35Z","timestamp":1384542155000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies"],"prefix":"10.1186","volume":"6","author":[{"given":"Eshita","family":"Mutt","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sudha Sane","family":"Rani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramanathan","family":"Sowdhamini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,11,15]]},"reference":[{"key":"98_CR1","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The protein data bank. Nucl Acid Res. 2000, 28: 235-242. 10.1093\/nar\/28.1.235.","journal-title":"Nucl Acid Res"},{"key":"98_CR2","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1016\/S0969-2126(97)00260-8","volume":"5","author":"CA Orengo","year":"1997","unstructured":"Orengo CA, Michie AD, Jones DT, Swindells MB, Thornton JM: CATH: a hierarchic classification of protein domain structures. Structure. 1997, 5: 1093-1108. 10.1016\/S0969-2126(97)00260-8. ISSN: 0969\u20132126","journal-title":"Structure"},{"key":"98_CR3","first-page":"536","volume":"247","author":"AG Murzin","year":"1995","unstructured":"Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995, 247: 536-540.","journal-title":"J Mol Biol"},{"key":"98_CR4","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/1471-2105-5-35","volume":"5","author":"A Bhaduri","year":"2004","unstructured":"Bhaduri A, Pugalenthi G, Sowdhamini R: PASS2: an automated database of protein alignments organised as structural superfamilies. BMC Bioinforma. 2004, 5: 35-10.1186\/1471-2105-5-35.","journal-title":"BMC Bioinforma"},{"issue":"1","key":"98_CR5","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1093\/nar\/30.1.284","volume":"30","author":"V Mallika","year":"2002","unstructured":"Mallika V, Bhaduri A, Sowdhamini R: PASS2: a semi-automated database of protein alignments organised as structural superfamilies. Nucleic Acids Res. 2002, 30 (1): 284-288. 10.1093\/nar\/30.1.284.","journal-title":"Nucleic Acids Res"},{"key":"98_CR6","volume-title":"Int J Knowl Discov Bioinform J","author":"K Kanagarajadurai","year":"2011","unstructured":"Kanagarajadurai K, Kalaimathy S, Nagarajan P, Sowdhamini R: PASS2: a database of structure-based sequence alignments of proteins structural domain superfamilies. Int J Knowl Discov Bioinform J. 2011, in press"},{"key":"98_CR7","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/1472-6807-8-28","volume":"8","author":"S Sandhya","year":"2008","unstructured":"Sandhya S, Pankaj B, Govind MK, Offmann B, Srinivasan N, Sowdhamini R: CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. BMC Struct Biol. 2008, 8: 28-10.1186\/1472-6807-8-28.","journal-title":"BMC Struct Biol"},{"issue":"3","key":"98_CR8","doi-asserted-by":"publisher","first-page":"e4981","DOI":"10.1371\/journal.pone.0004981","volume":"4","author":"S Sankaran","year":"2009","unstructured":"Sankaran S, Saane SR, Barah P, Madabosse KG, Offmann B, Srinivasan N, Sowdhamini R: Length variations amongst protein domain superfamilies and consequences on structure and function. PLoS One. 2009, 4 (3): e4981-10.1371\/journal.pone.0004981.","journal-title":"PLoS One"},{"issue":"7","key":"98_CR9","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1093\/bioinformatics\/14.7.617","volume":"14","author":"K Mizuguchi","year":"1998","unstructured":"Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP: JOY: protein sequence-structure representation and analysis. Bioinformatics. 1998, 14 (7): 617-623. 10.1093\/bioinformatics\/14.7.617.","journal-title":"Bioinformatics"},{"key":"98_CR10","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1098\/rspb.1990.0077","volume":"24","author":"JP Overington","year":"1990","unstructured":"Overington JP, Johnson MS, Sali A, Blundell TL: Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc R Suc Lond B. 1990, 24: 132-145.","journal-title":"Proc R Suc Lond B"},{"key":"98_CR11","volume-title":"Nature Protocols Network","author":"K Kanagarajadurai","year":"2009","unstructured":"Kanagarajadurai K, Kalaimathy S, Nagarajan P, Sowdhamini R: A bioinformatics protocol for rigorous structure-based sequence alignment of distantly related proteins. Nature Protocols Network. 2009,http:\/\/www.nature.com\/protocolexchange\/protocols\/604,"},{"key":"98_CR12","doi-asserted-by":"publisher","first-page":"29073","DOI":"10.1074\/jbc.M504215200","volume":"280","author":"A Schiefner","year":"2005","unstructured":"Schiefner A, Gerber K, Seitz S, Welte W, Diederichs K, Boos W: The crystal structure of Mlc, a global regulator of sugar metabolism in Escherichia coli. J Biol Chem. 2005, 280: 29073-29079. 10.1074\/jbc.M504215200.","journal-title":"J Biol Chem"},{"key":"98_CR13","doi-asserted-by":"publisher","first-page":"8894","DOI":"10.1021\/bi049083c","volume":"43","author":"O Kristensen","year":"2004","unstructured":"Kristensen O, Laurberg M, Liljas A, Kastrup JS, Gajhede M: Structural characterization of the stringent response related exopolyphosphatase\/guanosine Pentaphosphate phosphohydrolase protein family. Biochemistry. 2004, 43: 8894-8900. 10.1021\/bi049083c.","journal-title":"Biochemistry"},{"key":"98_CR14","doi-asserted-by":"publisher","first-page":"50591","DOI":"10.1074\/jbc.M408126200","volume":"279","author":"T Mukai","year":"2004","unstructured":"Mukai T, Kawai S, Mori S, Mikami B, Murata K: Crystal structure of bacterial inorganic polyphosphate\/ATP-glucomannokinase. Insights into kinase evolution. J Biol Chem. 2004, 279: 50591-50600. 10.1074\/jbc.M408126200.","journal-title":"J Biol Chem"},{"key":"98_CR15","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1107\/S1744309109022192","volume":"66","author":"Q Xu","year":"2010","unstructured":"Xu Q: Structure of an essential bacterial protein YeaZ (TM0874) from thermotoga maritima at 2.5\u00c5 Resolution. Acta Crystallogr Sect F. 2010, 66: 1230-1236. 10.1107\/S1744309109022192.","journal-title":"Acta Crystallogr Sect F"},{"key":"98_CR16","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1016\/j.jmb.2006.08.085","volume":"364","author":"WA Weihofen","year":"2006","unstructured":"Weihofen WA, Berger M, Chen H, Saenger W, Hinderlich S: Structures of human N-acetylglucosamine kinase in two complexes with N-acetylglucosamine and with ADP\/glucose: insights into substrate specificity and regulation. J Mol Biol. 2006, 364: 388-10.1016\/j.jmb.2006.08.085.","journal-title":"J Mol Biol"},{"key":"98_CR17","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/35092500","volume":"413","author":"F van den Ent","year":"2001","unstructured":"van den Ent F, Amos LA, Lowe J: Prokaryotic origin of the actin cytoskeleton. Nature. 2001, 413: 39-44. 10.1038\/35092500.","journal-title":"Nature"},{"key":"98_CR18","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1038\/sj.embor.7400448","volume":"6","author":"Y Zhu","year":"2005","unstructured":"Zhu Y, Huang W, Lee SS, Xu W: Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis. Embo Rep. 2005, 6: 681-687. 10.1038\/sj.embor.7400448.","journal-title":"Embo Rep"},{"key":"98_CR19","doi-asserted-by":"publisher","first-page":"1054","DOI":"10.1038\/nsmb850","volume":"11","author":"A Vila-Sanjurjo","year":"2004","unstructured":"Vila-Sanjurjo A, Schuwirth BS, Hau CW, Cate JH: Structural basis for the control of translation initiation during stress. Nat Struct Mol Biol. 2004, 11: 1054-1059. 10.1038\/nsmb850.","journal-title":"Nat Struct Mol Biol"},{"key":"98_CR20","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1038\/nature01922","volume":"425","author":"WN Zagotta","year":"2003","unstructured":"Zagotta WN, Olivier NB, Black KD, Young EC, Olson R, Gouaux JE: Structural basis for modulation and agonist specificity of HCN pacemaker channels. Nature. 2003, 425: 200-205. 10.1038\/nature01922.","journal-title":"Nature"},{"key":"98_CR21","unstructured":"Joint Center for Structural Genomics (JCSG): Crystal structure of transcription regulator from Bacteroides thetaiotaomicron VPI-5482 at 2.15 A resolution. To be published"},{"key":"98_CR22","unstructured":"Rotella FJ, Zhang RG, Mulligan R, Moy S, Joachimiak A: The 1.9-A crystal structure of transcriptional regulator, Crp\/Fnr family from Porphyromonas gingivalis. To be published"},{"issue":"2","key":"98_CR23","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1093\/bib\/bbq025","volume":"12","author":"S Kalaimathy","year":"2010","unstructured":"Kalaimathy S, Sowdhamini R, Kanagarajadurai K: Critical assessment of structure-based sequence alignment methods at distant relationships. Briefings in Bioinform. 2010, 12 (2): 163-175.","journal-title":"Briefings in Bioinform"},{"key":"98_CR24","doi-asserted-by":"publisher","first-page":"D189","DOI":"10.1093\/nar\/gkh034","volume":"32","author":"JM Chandonia","year":"2004","unstructured":"Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE: The ASTRAL compendium in 2004. Nucleic Acids Res. 2004, 32: D189-D192. 10.1093\/nar\/gkh034.","journal-title":"Nucleic Acids Res"},{"key":"98_CR25","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1002\/pro.5560030317","volume":"3","author":"U Hobohm","year":"1994","unstructured":"Hobohm U, Sander C: Enlarged representative set of protein structures. Protein Sci. 1994, 3: 522-524.","journal-title":"Protein Sci"},{"key":"98_CR26","volume-title":"Nucleic Acids Research","author":"E Mutt","year":"2013","unstructured":"Mutt E, Mathew OK, Sowdhamini R: LenVarDB: database of length-variant protein domains. Nucleic Acids Research. 2013, doi: 10.1093\/nar\/gkt1014"}],"container-title":["BioData Mining"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1756-0381-6-20.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1756-0381-6-20\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1756-0381-6-20","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1756-0381-6-20.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T02:20:55Z","timestamp":1630549255000},"score":1,"resource":{"primary":{"URL":"https:\/\/biodatamining.biomedcentral.com\/articles\/10.1186\/1756-0381-6-20"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11,15]]},"references-count":26,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["98"],"URL":"https:\/\/doi.org\/10.1186\/1756-0381-6-20","relation":{},"ISSN":["1756-0381"],"issn-type":[{"value":"1756-0381","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,11,15]]},"assertion":[{"value":"24 July 2012","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 September 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 November 2013","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"20"}}