{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T12:32:50Z","timestamp":1742387570868},"publisher-location":"Berlin, Heidelberg","reference-count":36,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642130779"},{"type":"electronic","value":"9783642130786"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010]]},"DOI":"10.1007\/978-3-642-13078-6_4","type":"book-chapter","created":{"date-parts":[[2010,5,8]],"date-time":"2010-05-08T15:28:37Z","timestamp":1273332517000},"page":"18-28","source":"Crossref","is-referenced-by-count":5,"title":["Touring Protein Space with Matt"],"prefix":"10.1007","author":[{"given":"Noah","family":"Daniels","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anoop","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matt","family":"Menke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"4_CR1","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"S. Altschul","year":"1997","unstructured":"Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., Lipman, L.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res.\u00a025, 3389\u20133402 (1997)","journal-title":"Nucleic Acids Res."},{"key":"4_CR2","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1093\/nar\/gkh039","volume":"32","author":"A. Andreeva","year":"2004","unstructured":"Andreeva, A., Howorth, D., Brenner, S., Hubbard, T., Chothia, C., Murzin, A.: SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Research\u00a032, D226\u2013D229 (2004)","journal-title":"Nucleic Acids Research"},{"key":"4_CR3","doi-asserted-by":"publisher","first-page":"2027","DOI":"10.1002\/pro.213","volume":"18","author":"C. Berbalk","year":"2009","unstructured":"Berbalk, C., Schwaiger, C., Lackner, P.: Accuracy analysis of multiple structure alignments. Protein Science\u00a018, 2027\u20132035 (2009)","journal-title":"Protein Science"},{"key":"4_CR4","unstructured":"Cheek, S., Qi, Y., Krishna, S., Kinch, L., Grishin, N.V.: SCOPmap: Automated assignment of protein structures to evolutionary superfamilies. BMC Bioinformatics\u00a07 (2006)"},{"key":"4_CR5","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/1471-2105-7-362","volume":"7","author":"P.-H. Chi","year":"2006","unstructured":"Chi, P.-H., Shyu, C.-R., Xu, D.: A fast SCOP fold classification system using content-based E-predict algorithm. BMC Bioinformatics\u00a07, 10.1186\/1471\u20132105\u20137\u2013362 (2006)","journal-title":"BMC Bioinformatics"},{"key":"4_CR6","doi-asserted-by":"publisher","first-page":"14056","DOI":"10.1073\/pnas.0606239103","volume":"103","author":"I.-G. Choi","year":"2006","unstructured":"Choi, I.-G., Kim, S.-H.: Evolution of protein structural classes and protein sequence families. Proc. Nat. Acad. Sci.\u00a0103, 14056\u201314061 (2006)","journal-title":"Proc. Nat. Acad. Sci."},{"key":"4_CR7","doi-asserted-by":"publisher","first-page":"2150","DOI":"10.1110\/ps.0306803","volume":"12","author":"R. Day","year":"2003","unstructured":"Day, R., Beck, D., Armen, R., Daggett, V.: A consensus view of fold space: Combining SCOP, CATH, and the Dali domain dictionary. Protein Science\u00a012, 2150\u20132160 (2003)","journal-title":"Protein Science"},{"key":"4_CR8","doi-asserted-by":"crossref","unstructured":"Gerstein, M., Levitt, M.: Comprehensive assement of automatic structural alignment against a manual standard, the SCOP classification of proteins. Protein Sci., 445\u2013456 (1998)","DOI":"10.1002\/pro.5560070226"},{"key":"4_CR9","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1002\/prot.1176","volume":"46","author":"G. Getz","year":"2002","unstructured":"Getz, G., Vendruscolo, M., Sachs, D., Domany, E.: Automatic assignment of SCOP and CATH protein structure classifications from FSSP scores. Proteins: Structure Function and Genetics\u00a046, 405\u2013415 (2002)","journal-title":"Proteins: Structure Function and Genetics"},{"key":"4_CR10","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1016\/S0959-440X(96)80058-3","volume":"6","author":"J. Gibrat","year":"2006","unstructured":"Gibrat, J., Madej, T., Bryant, S.: Suprising similarities in structure comparison. Curr. Opin. Struct. Biol.\u00a06, 377\u2013385 (2006)","journal-title":"Curr. Opin. Struct. Biol."},{"key":"4_CR11","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1093\/nar\/gkl959","volume":"35","author":"L. Greene","year":"2007","unstructured":"Greene, L., Lewis, T., Addou, S., Cuff, A., Dallman, T., Dibley, M., Redfern, O., Pearl, F., Nambudiry, R., Reid, A., Silitoe, I., Yeats, C., Thornton, J., Orengo, C.: The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res.\u00a035, D291\u2013D297 (2007)","journal-title":"Nucleic Acids Res."},{"key":"4_CR12","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1016\/S0969-2126(99)80177-4","volume":"7","author":"C. Hadley","year":"1999","unstructured":"Hadley, C., Jones, D.: A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure\u00a07, 1099\u20131112 (1999)","journal-title":"Structure"},{"key":"4_CR13","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 similarity within fold space. J. Mol. Bio.\u00a0323, 909\u2013926 (2002)","journal-title":"J. Mol. Bio."},{"key":"4_CR14","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1016\/j.jmb.2006.05.060","volume":"361","author":"T. Holland","year":"2006","unstructured":"Holland, T., Veretnik, S., Shindyalov, I.N., Bourne, P.: Partitioning protein structures into domains: why is it so difficult? J. Mol. Biol.\u00a0361, 562\u2013590 (2006)","journal-title":"J. Mol. Biol."},{"key":"4_CR15","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1093\/bioinformatics\/16.6.566","volume":"16","author":"L. Holm","year":"2000","unstructured":"Holm, L., Park, J.: DaliLite workbench for protein structure comparison. Bioinformatics\u00a016, 566\u2013567 (2000)","journal-title":"Bioinformatics"},{"key":"4_CR16","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1126\/science.273.5275.595","volume":"260","author":"L. Holm","year":"1996","unstructured":"Holm, L., Sander, C.: Mapping the protein universe. Science\u00a0260, 595\u2013602 (1996)","journal-title":"Science"},{"key":"4_CR17","doi-asserted-by":"crossref","unstructured":"Holm, L., Sander, C.: Touring protein fold space with Dali\/FSSP. Nucleic Acids Res., 316\u2013319 (1998)","DOI":"10.1093\/nar\/26.1.316"},{"key":"4_CR18","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1016\/j.sbi.2006.04.007","volume":"16","author":"R. Kolodny","year":"2006","unstructured":"Kolodny, R., Petrey, D., Honig, B.: Protein structure comparison: implications for the nature of fold space, and structure and function prediction. Curr. Opin. Struct. Biol.\u00a016, 393\u2013398 (2006)","journal-title":"Curr. Opin. Struct. Biol."},{"key":"4_CR19","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1002\/prot.340230309","volume":"23","author":"T. Madej","year":"1995","unstructured":"Madej, T., Gibrat, J.-F., Bryant, S.: Threading a database of protein cores. Proteins\u00a023, 356\u2013369 (1995)","journal-title":"Proteins"},{"issue":"1","key":"4_CR20","doi-asserted-by":"publisher","first-page":"10","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 Comput. Biol.\u00a04(1), e10 (2008) doi:10.1371\/journal.pcbi.0040010","journal-title":"PLoS Comput. Biol."},{"key":"4_CR21","first-page":"536","volume":"297","author":"A. Murzin","year":"1995","unstructured":"Murzin, A., Brenner, S., Hubbard, T., Chothia, C.: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol.\u00a0297, 536\u2013540 (1995)","journal-title":"J. Mol. Biol."},{"issue":"8","key":"4_CR22","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1016\/S0969-2126(97)00260-8","volume":"5","author":"C. Orengo","year":"1997","unstructured":"Orengo, C., Michie, A., Jones, S., Jones, D., Swindells, M., Thornton, J.: Cath- a hierarchic classification of protein domain structures. Structure\u00a05(8), 1093\u20131108 (1997)","journal-title":"Structure"},{"key":"4_CR23","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1093\/nar\/gkg062","volume":"31","author":"F. Pearl","year":"2003","unstructured":"Pearl, F., Bennett, C., Bray, J., Harrison, A., Martin, N., Shepherd, A., Sillitoe, I., Thornton, J., Orengo, C.: The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res.\u00a031, 452\u2013455 (2003)","journal-title":"Nucleic Acids Res."},{"key":"4_CR24","unstructured":"Redfern, O., Harrison, A., Dallman, T., Pearl, F., Orengo, C.: CATHEDRAL: A fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PLOS Computational Biology, e232 (2007) doi:10.1371\/journal.pcji.0030232"},{"key":"4_CR25","doi-asserted-by":"publisher","first-page":"1625","DOI":"10.1093\/bioinformatics\/btp296","volume":"25","author":"J. Rocha","year":"2009","unstructured":"Rocha, J., Segura, J., Wilson, R., Dasgupta, S.: Flexible structural protein alignment by a sequence of local transformations. Bioinformatics\u00a025, 1625\u20131631 (2009)","journal-title":"Bioinformatics"},{"key":"4_CR26","doi-asserted-by":"crossref","unstructured":"Rost, B.: Did evolution leap to create the protein universe? Curr. Opinion in Struct. Biol., 409\u2013416 (2002)","DOI":"10.1016\/S0959-440X(02)00337-8"},{"key":"4_CR27","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1016\/j.sbi.2009.04.009","volume":"19","author":"R. Sadreyev","year":"2009","unstructured":"Sadreyev, R., Kim, B.-H., Grishin, N.: Discrete-continous duality of protein structure space. Curr. Opinion Structural Biol.\u00a019, 321\u2013328 (2009)","journal-title":"Curr. Opinion Structural Biol."},{"key":"4_CR28","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1186\/1471-2105-7-206","volume":"7","author":"V. Sam","year":"2006","unstructured":"Sam, V., Tai, C., Garnier, J., Gibrat, J.F., Lee, B., Munson, P.: ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. BMC Bioinformatics\u00a07, 206 (2006)","journal-title":"BMC Bioinformatics"},{"key":"4_CR29","doi-asserted-by":"crossref","unstructured":"Sam, V., Tai, C., Garnier, J., Gibrat, J.F., Lee, B., Munson, P.: Towards an automatic classification of protein structural domains based on structural similarity. BMC Bioinformatics\u00a09 (2008)","DOI":"10.1186\/1471-2105-9-74"},{"key":"4_CR30","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1002\/(SICI)1097-0134(20000215)38:3<247::AID-PROT2>3.0.CO;2-T","volume":"38","author":"I. Shindyalov","year":"2000","unstructured":"Shindyalov, I., Bourne, P.: An alternative view of protein fold space. Proteins\u00a038, 513\u2013514 (2000)","journal-title":"Proteins"},{"key":"4_CR31","series-title":"Lecture Notes in Bioinformatics","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, C.N.S.: Rapid neighbour-joining. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol.\u00a05251, pp. 113\u2013122. Springer, Heidelberg (2008)"},{"key":"4_CR32","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1093\/bioinformatics\/btl594","volume":"23","author":"S. Suhrer","year":"2007","unstructured":"Suhrer, S., Wederstein, M., Sippl, M.: QSCOP-SCOP quantified by structural relationships. Bioinformatics\u00a023, 513\u2013514 (2007)","journal-title":"Bioinformatics"},{"key":"4_CR33","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.sbi.2009.03.011","volume":"19","author":"R. Valas","year":"2009","unstructured":"Valas, R., Yang, S., Bourne, P.: Nothing about protein structure classification makes sense except in the light of evolution. Curr. Opin. Struct. Biol.\u00a019, 329\u2013334 (2009)","journal-title":"Curr. Opin. Struct. Biol."},{"key":"4_CR34","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1016\/j.jmb.2004.03.053","volume":"339","author":"S. Veretnik","year":"2004","unstructured":"Veretnik, S., Bourne, P., Alexandrov, N., Shindyalov, I.: Toward consistent assignment of structural domains in proteins. J. Mol. Biol.\u00a0339, 647\u2013678 (2004)","journal-title":"J. Mol. Biol."},{"key":"4_CR35","first-page":"89","volume":"2","author":"M. Vuk","year":"2006","unstructured":"Vuk, M., Curk, T.: Roc curve, lift chart and calibration plot. Metodolo ski zvezki\u00a02, 89\u2013108 (2006)","journal-title":"Metodolo ski zvezki"},{"key":"4_CR36","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1093\/nar\/gkm1049","volume":"35","author":"A. Zemla","year":"2007","unstructured":"Zemla, A., Geisbrecht, B., Smith, J., Lam, M., Kirkpatrick, B., Wagner, M., Slezak, T., Zhou, C.: STRALCP\u2013structure alignment-based clustering of proteins. Nucleic Acids Res.\u00a035, e150 (2007)","journal-title":"Nucleic Acids Res."}],"container-title":["Lecture Notes in Computer Science","Bioinformatics Research and Applications"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-13078-6_4.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,24]],"date-time":"2020-11-24T03:00:54Z","timestamp":1606186854000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-13078-6_4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010]]},"ISBN":["9783642130779","9783642130786"],"references-count":36,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-13078-6_4","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2010]]}}}