{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,11]],"date-time":"2023-09-11T01:58:16Z","timestamp":1694397496632},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"S12","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1471-2105-15-s12-s2","type":"journal-article","created":{"date-parts":[[2014,11,6]],"date-time":"2014-11-06T16:03:02Z","timestamp":1415289782000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Discovering co-occurring patterns and their biological significance in protein families"],"prefix":"10.1186","volume":"15","author":[{"given":"En-Shiun Annie","family":"Lee","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sanderz","family":"Fung","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ho-Yin","family":"Sze-To","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew K C","family":"Wong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2014,11,6]]},"reference":[{"issue":"2","key":"6673_CR1","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1006\/jmbi.1996.0167","volume":"257","author":"O Lichtarge","year":"1996","unstructured":"Lichtarge O, Bourne HR, Cohen FE: An evolutionary trace method defines binding surfaces common to protein families. Journal of molecular biology. 1996, 257 (2): 342-358. 10.1006\/jmbi.1996.0167.","journal-title":"Journal of molecular biology"},{"issue":"22","key":"6673_CR2","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research. 1994, 22 (22): 4673-4680. 10.1093\/nar\/22.22.4673.","journal-title":"Nucleic acids research"},{"key":"6673_CR3","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","volume":"302","author":"C Notredame","year":"2000","unstructured":"Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of molecular biology. 2000, 302: 205-217. 10.1006\/jmbi.2000.4042.","journal-title":"Journal of molecular biology"},{"issue":"3","key":"6673_CR4","doi-asserted-by":"publisher","first-page":"e18093","DOI":"10.1371\/journal.pone.0018093","volume":"6","author":"JD Thompson","year":"2011","unstructured":"Thompson JD, Linard B, Lecompte O, Poch O: A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PloS one. 2011, 6 (3): e18093-10.1371\/journal.pone.0018093.","journal-title":"PloS one"},{"issue":"4","key":"6673_CR5","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1089\/cmb.1994.1.337","volume":"1","author":"L Wang","year":"1994","unstructured":"Wang L, Jiang T: On the complexity of multiple sequence alignment. Journal of computational biology. 1994, 1 (4): 337-348. 10.1089\/cmb.1994.1.337.","journal-title":"Journal of computational biology"},{"key":"6673_CR6","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1073\/pnas.0805923106","volume":"106","author":"M Weigt","year":"2009","unstructured":"Weigt M, White RA, Szurmant H, Hoch JA, Hwa T: Identification of direct residue contacts in protein-protein interaction by message passing. Proceedings of the National Academy of Sciences. 2009, 106: 67-72. 10.1073\/pnas.0805923106.","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"6673_CR7","doi-asserted-by":"publisher","first-page":"e1000633","DOI":"10.1371\/journal.pcbi.1000633","volume":"6","author":"L Burger","year":"2010","unstructured":"Burger L, van Nimwegen E: Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS computational biology. 2010, 6: e1000633-10.1371\/journal.pcbi.1000633.","journal-title":"PLoS computational biology"},{"issue":"49","key":"6673_CR8","doi-asserted-by":"publisher","first-page":"E1293","DOI":"10.1073\/pnas.1111471108","volume":"108","author":"F Morcos","year":"2011","unstructured":"Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M: Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proceedings of the National Academy of Sciences. 2011, 108 (49): E1293-E1301. 10.1073\/pnas.1111471108.","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"9","key":"6673_CR9","doi-asserted-by":"publisher","first-page":"8126","DOI":"10.1074\/jbc.M312671200","volume":"279","author":"S Madabushi","year":"2004","unstructured":"Madabushi S, Gross AK, Philippi A, Meng EC, Wensel TG, Lichtarge O: Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions. Journal of Biological Chemistry. 2004, 279 (9): 8126-8132. 10.1074\/jbc.M312671200.","journal-title":"Journal of Biological Chemistry"},{"key":"6673_CR10","volume-title":"Proteome Science","author":"ESA Lee","year":"2013","unstructured":"Lee ESA, Wong AKC: Revealing Binding Segments in Protein Families using Aligned Pattern Clusters. Proteome Science. 2013"},{"key":"6673_CR11","volume-title":"Scientifica","author":"X Xia","year":"2012","unstructured":"Xia X: Position weight matrix, gibbs sampler, and the associated significance tests in motif characterization and prediction. Scientifica. 2012, 2012:"},{"issue":"suppl 1","key":"6673_CR12","doi-asserted-by":"publisher","first-page":"D211","DOI":"10.1093\/nar\/gkp985","volume":"38","author":"RD Finn","year":"2010","unstructured":"Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K: The Pfam protein families database. Nucleic acids research. 2010, 38 (suppl 1): D211-D222.","journal-title":"Nucleic acids research"},{"issue":"D1","key":"6673_CR13","doi-asserted-by":"publisher","first-page":"D191","DOI":"10.1093\/nar\/gkt1140","volume":"42","author":"U Consortium","year":"2014","unstructured":"Consortium U: Activities at the Universal Protein Resource (UniProt). Nucleic Acids Research. 2014, 42 (D1): D191-D198.","journal-title":"Nucleic Acids Research"},{"issue":"8","key":"6673_CR14","doi-asserted-by":"publisher","first-page":"1408","DOI":"10.1109\/TKDE.2011.100","volume":"24","author":"AK Wong","year":"2012","unstructured":"Wong AK, Zhuang D, Li GC, Lee ES: Discovery of Delta Closed Patterns and Noninduced Patterns from Sequences. Knowledge and Data Engineering, IEEE Transactions on. 2012, 24 (8): 1408-1421.","journal-title":"Knowledge and Data Engineering, IEEE Transactions on"},{"issue":"4","key":"6673_CR15","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1007\/s11222-007-9033-z","volume":"17","author":"U Von Luxburg","year":"2007","unstructured":"Von Luxburg U: A tutorial on spectral clustering. Statistics and computing. 2007, 17 (4): 395-416. 10.1007\/s11222-007-9033-z.","journal-title":"Statistics and computing"},{"key":"6673_CR16","volume-title":"BIBM","author":"ESA Lee","year":"2013","unstructured":"Lee ESA, Fung S, Sze-To HY, Wong AK: Confirming biological significance of co-occurrence clusters of aligned pattern clusters. BIBM. 2013, p.(To Appear)"},{"key":"6673_CR17","volume-title":"Introduction to Data Mining","author":"PN Tan","year":"2006","unstructured":"Tan PN, Steinbach M, Kumar V: Introduction to Data Mining. 2006, Addison-Wesley"},{"key":"6673_CR18","volume-title":"Pattern recognition and machine learning","author":"CM Bishop","year":"2006","unstructured":"Bishop CM: Pattern recognition and machine learning. 2006, springer New York, 1:"},{"key":"6673_CR19","first-page":"422","volume-title":"Bioinformatics and Biomedicine (BIBM)","author":"ES Lee","year":"2013","unstructured":"Lee ES, Fung S, Sze-To HY, Wong A: Confirming biological significance of co-occurrence clusters of aligned pattern clusters. Bioinformatics and Biomedicine (BIBM). 2013, 422-427. IEEE International Conference on 2013"},{"issue":"8","key":"6673_CR20","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1016\/j.patrec.2009.09.011","volume":"31","author":"AK Jain","year":"2010","unstructured":"Jain AK: Data clustering: 50 years beyond K-means. Pattern Recognition Letters. 2010, 31 (8): 651-666. 10.1016\/j.patrec.2009.09.011.","journal-title":"Pattern Recognition Letters"},{"key":"6673_CR21","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 T, Weissig H, Shindyalov IN, Bourne PE: The protein data bank. Nucleic acids research. 2000, 28: 235-242. 10.1093\/nar\/28.1.235.","journal-title":"Nucleic acids research"},{"issue":"13","key":"6673_CR22","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE: UCSF Chimera-a visualization system for exploratory research and analysis. Journal of computational chemistry. 2004, 25 (13): 1605-1612. 10.1002\/jcc.20084.","journal-title":"Journal of computational chemistry"},{"issue":"11","key":"6673_CR23","doi-asserted-by":"publisher","first-page":"3582","DOI":"10.1073\/pnas.82.11.3582","volume":"82","author":"S Vijay-Kumar","year":"1985","unstructured":"Vijay-Kumar S, Bugg CE, Wilkinson KD, Cook WJ: Three-dimensional structure of ubiquitin at 2.8 A resolution. Proceedings of the National Academy of Sciences. 1985, 82 (11): 3582-3585. 10.1073\/pnas.82.11.3582.","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"10","key":"6673_CR24","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1038\/nrm2767","volume":"10","author":"I Dikic","year":"2009","unstructured":"Dikic I, Wakatsuki S, Walters KJ: Ubiquitin-binding domains-from structures to functions. Nature reviews Molecular cell biology. 2009, 10 (10): 659-671. 10.1038\/nrm2767.","journal-title":"Nature reviews Molecular cell biology"},{"issue":"23","key":"6673_CR25","doi-asserted-by":"publisher","first-page":"7300","DOI":"10.1021\/bi00189a035","volume":"33","author":"TJ Burch","year":"1994","unstructured":"Burch TJ, Haas AL: Site-directed mutagenesis of ubiquitin. Differential roles for arginine in the interaction with ubiquitin-activating enzyme. Biochemistry. 1994, 33 (23): 7300-7308. 10.1021\/bi00189a035.","journal-title":"Biochemistry"},{"issue":"13","key":"6673_CR26","doi-asserted-by":"crossref","first-page":"6396","DOI":"10.1016\/S0021-9258(18)45583-4","volume":"262","author":"S Vijay-Kumar","year":"1987","unstructured":"Vijay-Kumar S, Bugg C, Wilkinson K, Vierstra R, Hatfield P, Cook W: Comparison of the three-dimensional structures of human, yeast, and oat ubiquitin. Journal of Biological Chemistry. 1987, 262 (13): 6396-6399.","journal-title":"Journal of Biological Chemistry"},{"key":"6673_CR27","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1021\/bi0614838","volume":"46","author":"D Temp\u00b4e","year":"2007","unstructured":"Temp\u00b4e D, Brengues M, Mayonove P, Bensaad H, Lacrouts C, Morris MC: The alpha helix of ubiquitin interacts with yeast cyclin-dependent kinase subunit CKS1. Biochemistry. 2007, 46: 45-54. 10.1021\/bi0614838.","journal-title":"Biochemistry"},{"issue":"2","key":"6673_CR28","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1007\/s00018-013-1341-1","volume":"71","author":"S Zaidi","year":"2014","unstructured":"Zaidi S, Hassan MI, Islam A, Ahmad F: The role of key residues in structure, function, and stability of cytochrome-c. Cellular and Molecular Life Sciences. 2014, 71 (2): 229-255. 10.1007\/s00018-013-1341-1.","journal-title":"Cellular and Molecular Life Sciences"},{"issue":"11","key":"6673_CR29","doi-asserted-by":"publisher","first-page":"6371","DOI":"10.1073\/pnas.77.11.6371","volume":"77","author":"T Takano","year":"1980","unstructured":"Takano T, Dickerson RE: Redox conformation changes in refined tuna cytochrome c. Proceedings of the National Academy of Sciences. 1980, 77 (11): 6371-6375. 10.1073\/pnas.77.11.6371.","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"6673_CR30","volume-title":"West Indian Medical Journal","author":"V Sampson","year":"2009","unstructured":"Sampson V, Alleyne T, Ashe D: Probing the Specifics of Substrate Binding for Cytochrome c Oxidase A Computer Assisted Approach. West Indian Medical Journal. 2009, 58:"},{"issue":"8","key":"6673_CR31","doi-asserted-by":"publisher","first-page":"2647","DOI":"10.1016\/j.bpj.2010.08.042","volume":"99","author":"O Kokhan","year":"2010","unstructured":"Kokhan O, Wraight CA, Tajkhorshid E: The Binding Interface of Cytochrome c and Cytochrome c1 in the bc1 Complex: Rationalizing the Role of Key Residues. Biophysical journal. 2010, 99 (8): 2647-2656. 10.1016\/j.bpj.2010.08.042.","journal-title":"Biophysical journal"},{"issue":"12","key":"6673_CR32","doi-asserted-by":"publisher","first-page":"R281","DOI":"10.1016\/S0969-2126(00)88334-3","volume":"7","author":"PD Barker","year":"1999","unstructured":"Barker PD, Ferguson SJ: Still a puzzle: why is haem covalently attached in c-type cytochromes?. Structure. 1999, 7 (12): R281-R290. 10.1016\/S0969-2126(00)88334-3.","journal-title":"Structure"},{"issue":"6","key":"6673_CR33","doi-asserted-by":"publisher","first-page":"1118","DOI":"10.1039\/b717196j","volume":"25","author":"SE Bowman","year":"2008","unstructured":"Bowman SE, Bren KL: The chemistry and biochemistry of heme c: functional bases for covalent attachment. Natural product reports. 2008, 25 (6): 1118-1130. 10.1039\/b717196j.","journal-title":"Natural product reports"},{"issue":"4","key":"6673_CR34","doi-asserted-by":"publisher","first-page":"1372","DOI":"10.1021\/bi011371a","volume":"41","author":"SJ Hagen","year":"2002","unstructured":"Hagen SJ, Latypov RF, Dolgikh DA, Roder H: Rapid intrachain binding of histidine-26 and histidine-33 to heme in unfolded ferrocytochrome c. Biochemistry. 2002, 41 (4): 1372-1380. 10.1021\/bi011371a.","journal-title":"Biochemistry"},{"key":"6673_CR35","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1016\/0022-2836(81)90528-3","volume":"153","author":"T Takano","year":"1981","unstructured":"Takano T, Dickerson RE: Conformation change of cytochrome c: I. Ferrocytochrome c structure refined at 1 \u2022 5 A resolution. Journal of molecular biology. 1981, 153: 79-94. 10.1016\/0022-2836(81)90528-3.","journal-title":"Journal of molecular biology"},{"issue":"26","key":"6673_CR36","doi-asserted-by":"crossref","first-page":"15199","DOI":"10.1016\/S0021-9258(19)84810-X","volume":"264","author":"C Wallace","year":"1989","unstructured":"Wallace C, Mascagni P, Chait B, Collawn J, Paterson Y, Proudfoot A, Kent S: Substitutions engineered by chemical synthesis at three conserved sites in mitochondrial cytochrome c. Thermodynamic and functional consequences. Journal of Biological Chemistry. 1989, 264 (26): 15199-15209.","journal-title":"Journal of Biological Chemistry"},{"issue":"48","key":"6673_CR37","doi-asserted-by":"publisher","first-page":"14733","DOI":"10.1021\/bi971595m","volume":"36","author":"CJ Wallace","year":"1997","unstructured":"Wallace CJ, Clark-Lewis I: A rationale for the absolute conservation of Asn70 and Pro71 in mitochondrial cytochromes c suggested by protein engineering. Biochemistry. 1997, 36 (48): 14733-14740. 10.1021\/bi971595m.","journal-title":"Biochemistry"},{"issue":"3","key":"6673_CR38","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1139\/O07-049","volume":"85","author":"KM Black","year":"2007","unstructured":"Black KM, Wallace CJ: Probing the role of the conserved \u03b2-II turn Pro-76\/Gly-77 of mitochondrial cytochrome c. Biochemistry and cell biology. 2007, 85 (3): 366-374. 10.1139\/O07-049.","journal-title":"Biochemistry and cell biology"},{"issue":"20","key":"6673_CR39","doi-asserted-by":"publisher","first-page":"7870","DOI":"10.1021\/bi00420a043","volume":"27","author":"GV Louie","year":"1988","unstructured":"Louie GV, Pielak GJ, Smith M, Brayer GD: Role of phenylalanine-82 in yeast iso-1-cytochrome c and remote conformational changes induced by a serine residue at this position. Biochemistry. 1988, 27 (20): 7870-7876. 10.1021\/bi00420a043.","journal-title":"Biochemistry"},{"issue":"3","key":"6673_CR40","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1007\/s00775-012-0973-1","volume":"18","author":"TM Josephs","year":"2013","unstructured":"Josephs TM, Liptak MD, Hughes G, Lo A, Smith RM, Wilbanks SM, Bren KL, Ledgerwood EC: Conformational change and human cytochrome c function: mutation of residue 41 modulates caspase activation and destabilizes Met-80 coordination. JBIC Journal of Biological Inorganic Chemistry. 2013, 18 (3): 289-297. 10.1007\/s00775-012-0973-1.","journal-title":"JBIC Journal of Biological Inorganic Chemistry"},{"issue":"7","key":"6673_CR41","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1016\/S0969-2126(01)00205-2","volume":"3","author":"R Sanishvili","year":"1995","unstructured":"Sanishvili R, Volz K, Westbrook E, Margoliash E: The low ionic strength crystal structure of horse cytochrome c at 2.1 a resolution and comparison with its high ionic strength counterpart. Structure. 1995, 3 (7): 707-716. 10.1016\/S0969-2126(01)00205-2.","journal-title":"Structure"},{"key":"6673_CR42","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1042\/bj3020095","volume":"302","author":"A Schejter","year":"1994","unstructured":"Schejter A, Koshy T, Luntz T, Sanishvili R, Vig I, Margoliash E: Effects of mutating Asn-52 to isoleucine on the haem-linked properties of cytochrome c. Biochem J. 1994, 302: 95-101.","journal-title":"Biochem J"},{"issue":"3","key":"6673_CR43","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1021\/bi00054a026","volume":"32","author":"ZL Fredericks","year":"1993","unstructured":"Fredericks ZL, Pielak GJ: Exploring the interface between the N-and C-terminal helixes of cytochrome c by random mutagenesis within the C-terminal helix. Biochemistry. 1993, 32 (3): 929-936. 10.1021\/bi00054a026.","journal-title":"Biochemistry"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-S12-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,21]],"date-time":"2022-04-21T14:51:26Z","timestamp":1650552686000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-S12-S2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,6]]},"references-count":43,"journal-issue":{"issue":"S12","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6673"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-s12-s2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,6]]},"assertion":[{"value":"6 November 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S2"}}