{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,7,10]],"date-time":"2023-07-10T01:42:18Z","timestamp":1688953338142},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"S2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,1]]},"DOI":"10.1186\/1471-2105-15-s2-s1","type":"journal-article","created":{"date-parts":[[2014,1,24]],"date-time":"2014-01-24T18:02:54Z","timestamp":1390586574000},"source":"Crossref","is-referenced-by-count":1,"title":["Automatic classification of protein structures using low-dimensional structure space mappings"],"prefix":"10.1186","volume":"15","author":[{"given":"Daniel","family":"Asarnow","sequence":"first","affiliation":[]},{"given":"Rahul","family":"Singh","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,1,24]]},"reference":[{"key":"6272_CR1","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1093\/nar\/27.1.275","volume":"27","author":"C Orengo","year":"1999","unstructured":"Orengo C, Pearl F, Bray J, Todd A, Martin A, Lo Conte L, Thornton J: The CATH Database provides insights into protein structure\/function relationships. Nucleic Acids Research. 1999, 27: 275-279. 10.1093\/nar\/27.1.275.","journal-title":"Nucleic Acids Research"},{"key":"6272_CR2","doi-asserted-by":"publisher","first-page":"D419","DOI":"10.1093\/nar\/gkm993","volume":"36","author":"A Andreeva","year":"2007","unstructured":"Andreeva A, Howorth D, Chandonia J-M, Brenner SE, Hubbard TJP, Chothia C, Murzin AG: Data growth and its impact on the SCOP database: new developments. Nucleic Acids Research. 2007, 36: D419-D425. 10.1093\/nar\/gkm993.","journal-title":"Nucleic Acids Research"},{"key":"6272_CR3","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/1472-6807-9-23","volume":"9","author":"G Csaba","year":"2009","unstructured":"Csaba G, Birzele F, Zimmer R: Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis. BMC Structural Biology. 2009, 9: 23-10.1186\/1472-6807-9-23.","journal-title":"BMC Structural Biology"},{"key":"6272_CR4","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1093\/protein\/6.5.485","volume":"6","author":"CA Orengo","year":"1993","unstructured":"Orengo CA, Flores TP, Taylor WR, Thornton JM: Identification and classification of protein fold families. Protein Engineering. 1993, 6: 485-500. 10.1093\/protein\/6.5.485.","journal-title":"Protein Engineering"},{"key":"6272_CR5","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1126\/science.273.5275.595","volume":"273","author":"L Holm","year":"1996","unstructured":"Holm L, Sander C: Mapping the Protein Universe. Science. 1996, 273: 595-602. 10.1126\/science.273.5275.595.","journal-title":"Science"},{"key":"6272_CR6","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1016\/S0022-2836(02)00992-0","volume":"323","author":"A Harrison","year":"2002","unstructured":"Harrison A, Pearl F, Mott R, Thornton J, Orengo C: Quantifying the Similarities within Fold Space. Journal of Molecular Biology. 2002, 323: 909-926. 10.1016\/S0022-2836(02)00992-0.","journal-title":"Journal of Molecular Biology"},{"key":"6272_CR7","doi-asserted-by":"publisher","first-page":"3481","DOI":"10.1073\/pnas.0914097107","volume":"107","author":"I Budowski-Tal","year":"2010","unstructured":"Budowski-Tal I, Nov Y, Kolodny R: FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately. Proceedings of the National Academy of Sciences of the United States of America. 2010, 107: 3481-3486. 10.1073\/pnas.0914097107.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"6272_CR8","doi-asserted-by":"publisher","first-page":"12301","DOI":"10.1073\/pnas.1102727108","volume":"108","author":"M Osadchy","year":"2011","unstructured":"Osadchy M, Kolodny R: Maps of protein structure space reveal a fundamental relationship between protein structure and function. Proceedings of the National Academy of Sciences of the United States of America. 2011, 108: 12301-12306. 10.1073\/pnas.1102727108.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"6272_CR9","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1093\/nar\/26.1.316","volume":"26","author":"L Holm","year":"1998","unstructured":"Holm L, Sander C: Touring protein fold space with Dali\/FSSP. Nucleic Acids Research. 1998, 26: 316-319. 10.1093\/nar\/26.1.316.","journal-title":"Nucleic Acids Research"},{"key":"6272_CR10","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1186\/1471-2105-9-74","volume":"9","author":"V Sam","year":"2008","unstructured":"Sam V, Tai C-H, Garnier J, Gibrat J-F, Lee B, Munson PJ: Towards an automatic classification of protein structural domains based on structural similarity. BMC Bioinformatics. 2008, 9: 74-10.1186\/1471-2105-9-74.","journal-title":"BMC Bioinformatics"},{"key":"6272_CR11","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1109\/TCBB.2011.70","volume":"9","author":"N Daniels","year":"2012","unstructured":"Daniels N, Kumar A, Cowen L, Menke M: Touring Protein Space with Matt. IEEE\/ACM Transactions on Computational Biology and Bioinformatics. 2012, 9: 286-293.","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"6272_CR12","doi-asserted-by":"publisher","first-page":"3651","DOI":"10.1073\/pnas.0409772102","volume":"102","author":"J Hou","year":"2005","unstructured":"Hou J, Jun S-R, Zhang C, Kim S-H: Global mapping of the protein structure space and application in structure-based inference of protein function. Proceedings of the National Academy of Sciences of the United States of America. 2005, 102: 3651-3656. 10.1073\/pnas.0409772102.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"Suppl 7","key":"6272_CR13","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/1753-6561-7-S7-S1","volume":"7","author":"DE Asarnow","year":"2013","unstructured":"Asarnow DE, Singh R: The impact of structural diversity and method parameters on maps of the protein universe. BMC Proceedings. 2013, 7 (Suppl 7): S1-10.1186\/1753-6561-7-S7-S1.","journal-title":"BMC Proceedings"},{"issue":"Suppl 14","key":"6272_CR14","doi-asserted-by":"publisher","first-page":"S10","DOI":"10.1186\/1471-2105-14-S14-S10","volume":"14","author":"R Singh","year":"2013","unstructured":"Singh R, Yang H, Dalziel B, Asarnow D, Murad W, Foote D, Gromley M, Stillman J, Fisher S: Towards Human-Computer Synergetic Analysis of Large-Scale Biological Data. BMC Bioinformatics. 2013, 14 (Suppl 14): S10-10.1186\/1471-2105-14-S14-S10.","journal-title":"BMC Bioinformatics"},{"key":"6272_CR15","doi-asserted-by":"publisher","first-page":"2983","DOI":"10.1093\/bioinformatics\/btq572","volume":"26","author":"A Prli\u0107","year":"2010","unstructured":"Prli\u0107 A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE: Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics. 2010, 26: 2983-2985. 10.1093\/bioinformatics\/btq572.","journal-title":"Bioinformatics"},{"key":"6272_CR16","doi-asserted-by":"publisher","first-page":"D318","DOI":"10.1093\/nar\/gkp786","volume":"38","author":"S Griep","year":"2009","unstructured":"Griep S, Hobohm U: PDBselect 1992-2009 and PDBfilter-select. Nucleic Acids Research. 2009, 38: D318-D319.","journal-title":"Nucleic Acids Research"},{"key":"6272_CR17","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1093\/protein\/11.9.739","volume":"11","author":"IN Shindyalov","year":"1998","unstructured":"Shindyalov IN, Bourne PE: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering. 1998, 11: 739-747. 10.1093\/protein\/11.9.739.","journal-title":"Protein Engineering"},{"key":"6272_CR18","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1016\/S0968-0004(00)89105-7","volume":"20","author":"L Holm","year":"1995","unstructured":"Holm L, Sander C: Dali: a network tool for protein structure comparison. Trends in Biochemical Sciences. 1995, 20: 478-480. 10.1016\/S0968-0004(00)89105-7.","journal-title":"Trends in Biochemical Sciences"},{"key":"6272_CR19","doi-asserted-by":"crossref","first-page":"246ii","DOI":"10.1093\/bioinformatics\/btg1086","volume":"19","author":"Y Ye","year":"2003","unstructured":"Ye Y, Godzik A: Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. 2003, 19: 246ii-255.","journal-title":"Bioinformatics"},{"key":"6272_CR20","doi-asserted-by":"publisher","first-page":"e10","DOI":"10.1371\/journal.pcbi.0040010","volume":"4","author":"M Menke","year":"2008","unstructured":"Menke M, Berger B, Cowen L: Matt: Local Flexibility Aids Protein Multiple Structure Alignment. PLoS Computational Biology. 2008, 4: e10-10.1371\/journal.pcbi.0040010.","journal-title":"PLoS Computational Biology"},{"key":"6272_CR21","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1002\/(SICI)1097-0134(19981001)33:1<88::AID-PROT8>3.0.CO;2-H","volume":"33","author":"L Holm","year":"1998","unstructured":"Holm L, Sander C: Dictionary of recurrent domains in protein structures. Proteins: Structure, Function, and Bioinformatics. 1998, 33: 88-96. 10.1002\/(SICI)1097-0134(19981001)33:1<88::AID-PROT8>3.0.CO;2-H.","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"6272_CR22","doi-asserted-by":"publisher","first-page":"1841","DOI":"10.1110\/ps.03602304","volume":"13","author":"Y Ye","year":"2004","unstructured":"Ye Y, Godzik A: Database searching by flexible protein structure alignment. Protein Science. 2004, 13: 1841-1850. 10.1110\/ps.03602304.","journal-title":"Protein Science"},{"key":"6272_CR23","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1007\/BF02288916","volume":"17","author":"W Torgerson","year":"1952","unstructured":"Torgerson W: Multidimensional scaling: I. Theory and method. Psychometrika. 1952, 17: 401-419. 10.1007\/BF02288916.","journal-title":"Psychometrika"},{"key":"6272_CR24","first-page":"133","volume-title":"Recent Developments in Statistics","author":"J De Leeuw","year":"1977","unstructured":"De Leeuw J: Application of Convex Analysis to Multidimensional Scaling. Recent Developments in Statistics. 1977, Amsterdam: North-Holland Pub Co, 133-146."},{"key":"6272_CR25","volume-title":"ROC Graphs: Notes and Practical Considerations for Researchers","author":"T Fawcett","year":"2004","unstructured":"Fawcett T: ROC Graphs: Notes and Practical Considerations for Researchers. 2004"},{"key":"6272_CR26","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/978-3-540-87361-7_10","volume-title":"Algorithms in Bioinformatics","author":"M Simonsen","year":"2008","unstructured":"Simonsen M, Mailund T, Pedersen CNS: Rapid Neighbour-Joining. Algorithms in Bioinformatics. Edited by: Crandall KA, Lagergren J. 2008, Springer Berlin Heidelberg, 113-122."},{"key":"6272_CR27","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1186\/1756-0500-2-155","volume":"2","author":"W-H Chen","year":"2009","unstructured":"Chen W-H, Lercher MJ: ColorTree: a batch customization tool for phylogenic trees. BMC Research Notes. 2009, 2: 155-10.1186\/1756-0500-2-155.","journal-title":"BMC Research Notes"},{"key":"6272_CR28","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1093\/sysbio\/sys062","volume":"61","author":"DH Huson","year":"2012","unstructured":"Huson DH, Scornavacca C: Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. System Biology. 2012, 61: 1061-1067. 10.1093\/sysbio\/sys062.","journal-title":"System Biology"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-S2-S1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,10]],"date-time":"2023-07-10T01:10:28Z","timestamp":1688951428000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-S2-S1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1]]},"references-count":28,"journal-issue":{"issue":"S2","published-print":{"date-parts":[[2014,1]]}},"alternative-id":["6272"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-s2-s1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1]]},"article-number":"S1"}}