{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,5]],"date-time":"2025-10-05T04:29:19Z","timestamp":1759638559171},"publisher-location":"Berlin, Heidelberg","reference-count":25,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540332954"},{"type":"electronic","value":"9783540332961"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006]]},"DOI":"10.1007\/11732990_41","type":"book-chapter","created":{"date-parts":[[2006,3,28]],"date-time":"2006-03-28T12:59:27Z","timestamp":1143550767000},"page":"488-499","source":"Crossref","is-referenced-by-count":8,"title":["A Parameterized Algorithm for Protein Structure Alignment"],"prefix":"10.1007","author":[{"given":"Jinbo","family":"Xu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng","family":"Jiao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"issue":"6","key":"41_CR1","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1089\/cmb.2004.11.1061","volume":"11","author":"M. Comin","year":"2004","unstructured":"Comin, M., Guerra, C., Zanotti, G.: PROuST: a comparison method of three-dimensional structures of proteins using indexing techniques. Journal of Computational Biology\u00a011(6), 1061\u20131072 (2004)","journal-title":"Journal of Computational Biology"},{"key":"41_CR2","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1006\/jmbi.1993.1489","volume":"233","author":"L. Holm","year":"1993","unstructured":"Holm, L., Sander, C.: Protein structure comparison by alignment of distance matrices. Journal of Molecular Biology\u00a0233, 123\u2013138 (1993)","journal-title":"Journal of Molecular Biology"},{"key":"41_CR3","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1093\/protein\/9.9.727","volume":"9","author":"N.N. Alexandrov","year":"1996","unstructured":"Alexandrov, N.N.: SARFing the PDB. Protein Engineering\u00a09, 727\u2013732 (1996)","journal-title":"Protein Engineering"},{"key":"41_CR4","unstructured":"Gerstein, M., Levitt, M.: Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures. In: Proceedings of International Conference on Intelligent Systems in Molecular Biology, pp. 59\u201367 (1996)"},{"key":"41_CR5","unstructured":"Singh, A.P., Brutlag, D.L.: Hierarchical protein structure superposition using both secondary structure and atomic representations. In: Proceedings of International Conference on Intelligent Systems in Molecular Biology, pp. 284\u2013293 (1997)"},{"key":"41_CR6","doi-asserted-by":"crossref","unstructured":"Gibrat, J.F., Madej, T., Bryant, S.H.: Surprising similarities in structure comparison. Current Opinion in Structural Biology\u00a0(6), 377\u2013385 (1996)","DOI":"10.1016\/S0959-440X(96)80058-3"},{"key":"41_CR7","unstructured":"Akutsu, T., Tashimo, H.: Protein structure comparison using representation by line segment sequences. In: Proceedings of Pacific Symposium on Biocomputing 1996 (PSB 1996), pp. 25\u201340 (1996)"},{"key":"41_CR8","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1145\/369133.369199","volume-title":"RECOMB 2001","author":"G. Lancia","year":"2001","unstructured":"Lancia, G., Carr, R., Walenz, B., Istrail, S.: 101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem. In: RECOMB 2001, pp. 193\u2013202. ACM Press, New York (2001)"},{"key":"41_CR9","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1145\/565196.565209","volume-title":"RECOMB 2002","author":"A. Caprara","year":"2002","unstructured":"Caprara, A., Lancia, G.: Structural alignment of large\u2013size proteins via Lagrangian relaxation. In: RECOMB 2002, pp. 100\u2013108. ACM Press, New York (2002)"},{"key":"41_CR10","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-540-44827-3_1","volume-title":"Mathematical Methods for Protein Structure Analysis and Design","author":"G. Lancia","year":"2003","unstructured":"Lancia, G., Istrail, S.: Protein structure comparison: Algorithms and applications. In: Guerra, C., Istrail, S. (eds.) Mathematical Methods for Protein Structure Analysis and Design. LNCS (LNBI), vol.\u00a02666, pp. 1\u201333. Springer, Heidelberg (2003)"},{"key":"41_CR11","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1023\/A:1008194019144","volume":"14","author":"C. Lemmen","year":"2000","unstructured":"Lemmen, C., Lengauer, T.: Computational methods for the structural alignment of molecules. Journal of Computer-Aided Molecular Design\u00a014, 215\u2013232 (2000)","journal-title":"Journal of Computer-Aided Molecular Design"},{"issue":"33","key":"41_CR12","doi-asserted-by":"publisher","first-page":"12201","DOI":"10.1073\/pnas.0404383101","volume":"101","author":"R. Kolodny","year":"2004","unstructured":"Kolodny, R., Linial, N.: Approximate protein structural alignment in polynomial time. PNAS\u00a0101(33), 12201\u201312206 (2004)","journal-title":"PNAS"},{"key":"41_CR13","first-page":"512","volume-title":"FOCS 1999: Proceedings of the 40th Annual Symposium on Foundations of Computer Science","author":"D. Goldman","year":"1999","unstructured":"Goldman, D., Papadimitriou, C.H., Istrail, S.: Algorithmic aspects of protein structure similarity. In: FOCS 1999: Proceedings of the 40th Annual Symposium on Foundations of Computer Science, pp. 512\u2013522. IEEE Computer Society, Los Alamitos (1999)"},{"issue":"9","key":"41_CR14","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1093\/protein\/11.9.739","volume":"11","author":"I.N. Shindyalov","year":"1998","unstructured":"Shindyalov, I.N., Bourne, P.E.: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering\u00a011(9), 739\u2013747 (1998)","journal-title":"Protein Engineering"},{"key":"41_CR15","unstructured":"Verbitsky, O.: On the largest common subgraph problem (1994) (unpublished manuscript)"},{"key":"41_CR16","unstructured":"Jokisch, S., M\u00fcller, H.: Inter-point-distance-dependent approximate point set matching. Technical Report Research Report No. 653 (1997)"},{"key":"41_CR17","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1093\/bioinformatics\/bti128","volume":"27","author":"X. Yuan","year":"2005","unstructured":"Yuan, X., Bystroff, C.: Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. Bioinformatics\u00a027, 1010\u20131019 (2005)","journal-title":"Bioinformatics"},{"issue":"Suppl. 1","key":"41_CR18","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1093\/bioinformatics\/btg1012","volume":"19","author":"O. Dror","year":"2003","unstructured":"Dror, O., Benyamini, H., Nussinov, R., Wolfson, H.: MASS: Multiple structural alignment by secondary structures. Bioinformatics\u00a019(Suppl. 1), 95\u2013104 (2003)","journal-title":"Bioinformatics"},{"key":"41_CR19","doi-asserted-by":"crossref","unstructured":"Zhu, J., Weng, Z.: FAST: A novel protein structure alignment algorithm. Proteins: Structure Function, and Bioinformatics (in Press, 2004)","DOI":"10.1002\/prot.20331"},{"key":"41_CR20","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"H.M. Berman","year":"2000","unstructured":"Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Research\u00a028, 235\u2013242 (2000)","journal-title":"Nucleic Acids Research"},{"issue":"5","key":"41_CR21","doi-asserted-by":"publisher","first-page":"698","DOI":"10.1109\/TPAMI.1987.4767965","volume":"9","author":"K.S. Arun","year":"1987","unstructured":"Arun, K.S., Huang, T.S., Blostein, S.D.: Least-square fitting of two 3-d point sets. IEEE Trans. on Pattern Analysis and Machine Intelligence\u00a09(5), 698\u2013700 (1987)","journal-title":"IEEE Trans. on Pattern Analysis and Machine Intelligence"},{"key":"41_CR22","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1016\/0196-6774(86)90023-4","volume":"7","author":"N. Robertson","year":"1986","unstructured":"Robertson, N., Seymour, P.D.: Graph minors. II. algorithmic aspects of tree-width. Journal of Algorithms\u00a07, 309\u2013322 (1986)","journal-title":"Journal of Algorithms"},{"key":"41_CR23","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1007\/11415770_32","volume-title":"Research in Computational Molecular Biology","author":"J. Xu","year":"2005","unstructured":"Xu, J.: Rapid side-chain packing via tree decomposition. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol.\u00a03500, pp. 423\u2013439. Springer, Heidelberg (2005)"},{"key":"41_CR24","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1073\/pnas.89.14.6614","volume":"89","author":"M.H. Hao","year":"1992","unstructured":"Hao, M.H., Rackovsky, S., Liwo, A., Pincus, M.R., Scheraga, H.A.: Proc. Natl. Acad. Sci. USA\u00a089, 6614\u20136618 (1992)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"1","key":"41_CR25","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1089\/106652704773416876","volume":"11","author":"A. Caprara","year":"2004","unstructured":"Caprara, A., Carr, R., Istrail, S., Lancia, G., Walenz, B.: 101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem. Journal of Computational Biology\u00a011(1), 27\u201352 (2004)","journal-title":"Journal of Computational Biology"}],"container-title":["Lecture Notes in Computer Science","Research in Computational Molecular Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/11732990_41.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T06:52:55Z","timestamp":1619506375000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/11732990_41"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006]]},"ISBN":["9783540332954","9783540332961"],"references-count":25,"URL":"https:\/\/doi.org\/10.1007\/11732990_41","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2006]]}}}