{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,7,3]],"date-time":"2023-07-03T04:17:10Z","timestamp":1688357830909},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2013,7,12]],"date-time":"2013-07-12T00:00:00Z","timestamp":1373587200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Artif Intell Rev"],"published-print":{"date-parts":[[2014,10]]},"DOI":"10.1007\/s10462-013-9416-9","type":"journal-article","created":{"date-parts":[[2013,7,11]],"date-time":"2013-07-11T04:56:05Z","timestamp":1373518565000},"page":"445-459","source":"Crossref","is-referenced-by-count":1,"title":["Going over the three dimensional protein structure similarity problem"],"prefix":"10.1007","volume":"42","author":[{"given":"Nantia","family":"Iakovidou","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eleftherios","family":"Tiakas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Konstantinos","family":"Tsichlas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yannis","family":"Manolopoulos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,7,12]]},"reference":[{"key":"9416_CR1","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1093\/protein\/9.9.727","volume":"9","author":"NN Alexandrov","year":"1996","unstructured":"Alexandrov NN (1996) SARFing the PDB. Protein Eng 9:727\u2013732","journal-title":"Protein Eng"},{"key":"9416_CR2","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1093\/protein\/6.3.279","volume":"6","author":"O Bachar","year":"1993","unstructured":"Bachar O, Fischer D, Nussinov R, Wolfson H (1993) A computer vision based technique for 3D sequence-independent structural comparison of proteins. Protein Eng 6:279\u2013288","journal-title":"Protein Eng"},{"key":"9416_CR3","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.str.2006.11.009","volume":"15","author":"M Bashton","year":"2007","unstructured":"Bashton M, Chothia C (2007) The generation of new protein functions by the combination of domains. Structure 15:85\u201399","journal-title":"Structure"},{"key":"9416_CR4","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2007","unstructured":"Berman HM et al (2007) The protein data bank. Nucleic Acids Res 28:235\u2013242","journal-title":"Nucleic Acids Res"},{"key":"9416_CR5","doi-asserted-by":"crossref","first-page":"3481","DOI":"10.1073\/pnas.0914097107","volume":"107","author":"I Budowski-Tal","year":"2010","unstructured":"Budowski-Tal I, Nov Y, Kolodny R (2010) FragBag, an accurate representation of protein structure, retrieves stuctural neighbors from the entire PDB quickly and accurately. Proc Natl Acad Sci USA 107:3481\u20133486","journal-title":"Proc Natl Acad Sci USA"},{"key":"9416_CR6","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1142\/S0219720004000533","volume":"2","author":"T Can","year":"2004","unstructured":"Can T, Wang YF (2004) Protein structure alignment and fast similarity search using local shape signatures. J Bioinform Comput Biol 2:215\u2013239","journal-title":"J Bioinform Comput Biol"},{"key":"9416_CR7","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1006\/jmbi.2001.5250","volume":"315","author":"O Carugo","year":"2002","unstructured":"Carugo O, Pongor S (2002) Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison. J Mol Biol 315:887\u2013898","journal-title":"J Mol Biol"},{"key":"9416_CR8","unstructured":"Ciaccia P, Patella M, Zezula P (1997) M-tree: an efficient access method for similarity search in metric spaces. In: Proceedings of the 23rd international conference on very large databases (VLDB)"},{"key":"9416_CR9","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/0022-2836(80)90154-0","volume":"137","author":"FE Cohen","year":"1980","unstructured":"Cohen FE, Sternberg MJE (1980) Use of chemically derived distance constraints in the prediction of protein structure with myoglobin as an example. J Mol Biol 137:9\u201322","journal-title":"J Mol Biol"},{"key":"9416_CR10","doi-asserted-by":"crossref","first-page":"2492","DOI":"10.1110\/ps.03200603","volume":"12","author":"O Dror","year":"2003","unstructured":"Dror O, Benyamini H, Nussinov R, Wolfson HJ (2003) Multiple structural alignment by secondary structures: algorithm and applications. Protein Sci 12:2492\u2013507","journal-title":"Protein Sci"},{"key":"9416_CR11","unstructured":"Fischer D, Elofsson A, Rice D, Eisenberg D (1996) Assessing the performance of fold recognition methods by means of a comprehensive benchmark. In: Pacific symposium on biocomputing, pp 300\u2013318"},{"key":"9416_CR12","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.jmb.2006.11.017","volume":"366","author":"JH Fong","year":"2007","unstructured":"Fong JH, Geer LY, Panchenko AR, Bryant SH (2007) Modeling the evolution of protein domain architectures using maximum parsimony. J Mol Biol 366:307\u2013315","journal-title":"J Mol Biol"},{"key":"9416_CR13","doi-asserted-by":"crossref","first-page":"2781","DOI":"10.1016\/S0006-3495(02)75287-9","volume":"83","author":"HH Gan","year":"2002","unstructured":"Gan HH et al (2002) Analysis of protein sequence\/structure similarity relationships. Biophys J 83:2781\u20132791","journal-title":"Biophys J"},{"key":"9416_CR14","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/S0959-440X(96)80058-3","volume":"6","author":"JF Gibrat","year":"1996","unstructured":"Gibrat JF, Madej T, Bryant SH (1996) Surprising similarities in structure comparison. Curr Opin Struct Biol 6:377\u2013385","journal-title":"Curr Opin Struct Biol"},{"key":"9416_CR15","doi-asserted-by":"crossref","unstructured":"Griep S, Hobohm U (2010) PDBselect 1992\u20132009 and PDBfilter-select. Nucleic Acids Res Database Issue 38:318\u2013319","DOI":"10.1093\/nar\/gkp786"},{"key":"9416_CR16","doi-asserted-by":"crossref","first-page":"1374","DOI":"10.1110\/ps.035469.108","volume":"17","author":"A Guerler","year":"2008","unstructured":"Guerler A, Knapp EW (2008) Novel protein folds and their nonsequential structural analogs. Protein Sci 17:1374\u20131382","journal-title":"Protein Sci"},{"key":"9416_CR17","doi-asserted-by":"crossref","unstructured":"Guttman A (1984) R-trees: a dynamic index structure for spatial searching. In: Proceedings of the ACM SIGMOD conference, p 4757","DOI":"10.1145\/602259.602266"},{"key":"9416_CR18","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1006\/jmbi.1993.1489","volume":"233","author":"L Holm","year":"1993","unstructured":"Holm L, Sander C (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233:123\u2013138","journal-title":"J Mol Biol"},{"key":"9416_CR19","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1016\/S0959-440X(00)00214-1","volume":"11","author":"P Koehl","year":"2001","unstructured":"Koehl P (2001) Protein structure similarities. Curr Opin Struct Biol 11:348\u2013353","journal-title":"Curr Opin Struct Biol"},{"key":"9416_CR20","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1186\/1471-2105-7-510","volume":"7","author":"B Kolbeck","year":"2006","unstructured":"Kolbeck B, May P, Schmidt-Goenner T, Steinke T, Knapp EW (2006) Connectivity independent protein-structure alignment. BMC Bioinform 7:510\u2013510","journal-title":"BMC Bioinform"},{"key":"9416_CR21","first-page":"2256","volume":"60","author":"E Krissinel","year":"2004","unstructured":"Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr 60:2256\u20132268","journal-title":"Acta Crystallogr"},{"key":"9416_CR22","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1002\/prot.20921","volume":"64","author":"AS Konagurthu","year":"2006","unstructured":"Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM (2006) MUSTANG: a multiple structural alignment algorithm, proteins: structures. Funct Bioinform 64:559\u2013574","journal-title":"Funct Bioinform"},{"key":"9416_CR23","volume-title":"Introduction to protein science: architecture, function and genomics","author":"AM Lesk","year":"2004","unstructured":"Lesk AM (2004) Introduction to protein science: architecture, function and genomics. Oxford University Press, Oxford"},{"key":"9416_CR24","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/S0959-440X(02)00284-1","volume":"12","author":"O Lichtarge","year":"2002","unstructured":"Lichtarge O, Sowa ME (2002) Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol 12:21\u201327","journal-title":"Curr Opin Struct Biol"},{"key":"9416_CR25","doi-asserted-by":"crossref","first-page":"3255","DOI":"10.1093\/bioinformatics\/bti527","volume":"21","author":"D Lupyan","year":"2005","unstructured":"Lupyan D, Leo-Macias A, Ortiz AR (2005) A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics 21:3255\u20133263","journal-title":"Bioinformatics"},{"key":"9416_CR26","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1002\/prot.340230309","volume":"23","author":"T Madej","year":"1995","unstructured":"Madej T, Gibrat JF, Bryant SH (1995) Threading a database of protein cores. Proteins 23:356\u2013369","journal-title":"Proteins"},{"key":"9416_CR27","first-page":"2663","volume":"20","author":"C Micheletti","year":"2009","unstructured":"Micheletti C, Orland H (2009) MISTRAL: a tool for energy-based multiple structural alignment of proteins. Oxf Univ Press 20:2663\u20139","journal-title":"Oxf Univ Press"},{"key":"9416_CR28","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1016\/0022-2836(94)90017-5","volume":"236","author":"SC Mosimann","year":"1994","unstructured":"Mosimann SC, Ardelt W, James MNG (1994) Refined 1.7 a X-ray crystallographic structure of P-30 protein, an amphibian ribonuclease with anti-tumor activity. J Mol Biol 236:1141\u20131153","journal-title":"J Mol Biol"},{"key":"9416_CR29","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443\u2013453","journal-title":"J Mol Biol"},{"key":"9416_CR30","doi-asserted-by":"crossref","first-page":"2606","DOI":"10.1110\/ps.0215902","volume":"11","author":"AR Ortiz","year":"2002","unstructured":"Ortiz AR, Strauss CEM, Olmea O (2002) MAMMOTH: an automated method for model comparison. Protein Sci 11:2606\u20132621","journal-title":"Protein Sci"},{"key":"9416_CR31","doi-asserted-by":"crossref","unstructured":"Park C, Park S, Kim D, Park S, Sung M, Lee H, Shin J, Hwang C (2006) Fast protein structure alignment algorithm based on local geometric similarity. In: MICAI 2006, LNAI 4293, pp 1179\u20131189","DOI":"10.1007\/11925231_113"},{"key":"9416_CR32","doi-asserted-by":"crossref","first-page":"W41","DOI":"10.1093\/nar\/gkq293","volume":"38","author":"R Potestio","year":"2010","unstructured":"Potestio R, Aleksiev T, Pontiggia F, Cozzini S, Micheletti C (2010) ALADYN: a web server for aligning proteins by matching their large-scale motion. Nucleic Acids Res 38:W41\u2013W45","journal-title":"Nucleic Acids Res"},{"key":"9416_CR33","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1073\/pnas.2636460100","volume":"100","author":"P Rogen","year":"2003","unstructured":"Rogen P, Fain B (2003) Automatic classification of protein structure by using Gauss integrals. Proc Natl Acad Sci 100:119\u2013124","journal-title":"Proc Natl Acad Sci"},{"key":"9416_CR34","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1110\/ps.03239404","volume":"13","author":"J Shapiro","year":"2004","unstructured":"Shapiro J, Brutlag D (2004) FoldMiner: structural motif discovery using an improved superposition algorithm. Protein Sci 13:278\u2013294","journal-title":"Protein Sci"},{"key":"9416_CR35","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1002\/prot.10628","volume":"56","author":"M Shatsky","year":"2004","unstructured":"Shatsky M, Nussinov R, Wolfson HJ (2004) A method for simultaneous alignment of multiple protein structures. Proteins 56:143\u2013156","journal-title":"Proteins"},{"key":"9416_CR36","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1093\/protein\/11.9.739","volume":"11","author":"IN Shindyalov","year":"1998","unstructured":"Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11:739\u2013747","journal-title":"Protein Eng"},{"key":"9416_CR37","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1186\/1471-2105-11-446","volume":"11","author":"AD Stivala","year":"2010","unstructured":"Stivala AD, Stuckey PJ, Wirth AI (2010) Fast and accurate protein substructure searching with simulated annealing and GPUs. BMC Bioinform 11:446\u2013463","journal-title":"BMC Bioinform"},{"key":"9416_CR38","doi-asserted-by":"crossref","unstructured":"Traina C, Traina AJM, Seeger B, Faloutsos C (2000) Slim-trees: high performance metric trees minimizing overlap between nodes. In: Proceedings of the seventh international conference on extending database technology (EDBT), pp 51\u201365","DOI":"10.1007\/3-540-46439-5_4"},{"key":"9416_CR39","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1186\/1471-2105-9-358","volume":"9","author":"M Veeramalai","year":"2008","unstructured":"Veeramalai M, Ye Y, Godzik A (2008) TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinformatics 9:358","journal-title":"BMC Bioinformatics"},{"key":"9416_CR40","doi-asserted-by":"crossref","first-page":"5441","DOI":"10.1073\/pnas.0704422105","volume":"105","author":"L Xie","year":"2008","unstructured":"Xie L, Bourne PE (2008) Detecting evolutionary relationships across existing fold space. Proc Natl Acad Sci USA 105:5441\u20135446","journal-title":"Proc Natl Acad Sci USA"},{"key":"9416_CR41","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1093\/bioinformatics\/btg1086","volume":"19","author":"Y Ye","year":"2003","unstructured":"Ye Y, Godzik A (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19:246\u2013255","journal-title":"Bioinformatics"},{"key":"9416_CR42","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1093\/bioinformatics\/bti128","volume":"21","author":"X Yuan","year":"2005","unstructured":"Yuan X, Bystroff C (2005) Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. Bioinformatics 21:1010\u20131019","journal-title":"Bioinformatics"},{"key":"9416_CR43","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1110\/ps.073390208","volume":"17","author":"A Zen","year":"2008","unstructured":"Zen A, Carnevale V, Lesk AM, Micheletti C (2008) Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families. Protein Sci 17:918\u2013929","journal-title":"Protein Sci"},{"key":"9416_CR44","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1186\/1471-2105-7-460","volume":"7","author":"D Zhi","year":"2006","unstructured":"Zhi D, Krishna S, Cao H, Pevzner P, Godzik A (2006) Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinform 7:460\u2013475","journal-title":"BMC Bioinform"},{"key":"9416_CR45","doi-asserted-by":"crossref","first-page":"S46","DOI":"10.1186\/1471-2105-11-S1-S46","volume":"11","author":"L Zhang","year":"2010","unstructured":"Zhang L, Bailey J, Konagurthu AS, Ramamohanarao K (2010) A fast indexing approach for protein structure comparison. BMC Bioinform 11:S46","journal-title":"BMC Bioinform"}],"container-title":["Artificial Intelligence Review"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10462-013-9416-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10462-013-9416-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10462-013-9416-9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,3]],"date-time":"2023-07-03T02:17:42Z","timestamp":1688350662000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10462-013-9416-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,7,12]]},"references-count":45,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2014,10]]}},"alternative-id":["9416"],"URL":"https:\/\/doi.org\/10.1007\/s10462-013-9416-9","relation":{},"ISSN":["0269-2821","1573-7462"],"issn-type":[{"value":"0269-2821","type":"print"},{"value":"1573-7462","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,7,12]]}}}