{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T04:58:27Z","timestamp":1725512307930},"publisher-location":"Berlin, Heidelberg","reference-count":36,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540720300"},{"type":"electronic","value":"9783540720317"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1007\/978-3-540-72031-7_47","type":"book-chapter","created":{"date-parts":[[2007,8,5]],"date-time":"2007-08-05T14:16:24Z","timestamp":1186323384000},"page":"518-529","source":"Crossref","is-referenced-by-count":3,"title":["Delta: A Toolset for the Structural Analysis of Biological Sequences on a 3D Triangular Lattice"],"prefix":"10.1007","author":[{"given":"Minghui","family":"Jiang","sequence":"first","affiliation":[]},{"given":"Martin","family":"Mayne","sequence":"additional","affiliation":[]},{"given":"Joel","family":"Gillespie","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"issue":"10","key":"47_CR1","doi-asserted-by":"publisher","first-page":"3035","DOI":"10.1093\/nar\/18.10.3035","volume":"18","author":"J.P. Abrahams","year":"1990","unstructured":"Abrahams, J.P., et al.: Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Research\u00a018(10), 3035\u20133044 (1990)","journal-title":"Nucleic Acids Research"},{"doi-asserted-by":"crossref","unstructured":"Agarwala, R., et al.: Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. In: Proceedings of the 8th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA\u201997), pp. 390\u2013399 (1997)","key":"47_CR2","DOI":"10.1145\/267521.267522"},{"issue":"1-3","key":"47_CR3","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/S0166-218X(00)00186-4","volume":"104","author":"T. Akutsu","year":"2000","unstructured":"Akutsu, T.: Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Applied Mathematics\u00a0104(1-3), 45\u201362 (2000)","journal-title":"Discrete Applied Mathematics"},{"issue":"3","key":"47_CR4","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1006\/jtbi.1995.0098","volume":"174","author":"F.H.D. Batenburg van","year":"1995","unstructured":"van Batenburg, F.H.D., Gultyaev, A.P., Pleij, C.W.A.: An APL-programmed genetic algorithm for the prediction of RNA secondary structure. Journal of Theoretical Biology\u00a0174(3), 269\u2013280 (1995)","journal-title":"Journal of Theoretical Biology"},{"issue":"1","key":"47_CR5","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1093\/nar\/28.1.201","volume":"28","author":"F.H.D. Batenburg van","year":"2000","unstructured":"van Batenburg, F.H.D., et al.: Pseudobase: a database with RNA pseudoknots. Nucleic Acids Research\u00a028(1), 201\u2013204 (2000)","journal-title":"Nucleic Acids Research"},{"doi-asserted-by":"crossref","unstructured":"Berger, B., Leighton, T.: Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete. In: Proceedings of the 2nd Conference on Computational Molecular Biology (RECOMB\u201998), pp. 30\u201339 (1998)","key":"47_CR6","DOI":"10.1145\/279069.279080"},{"doi-asserted-by":"crossref","unstructured":"Crescenzi, P., et al.: On the complexity of protein folding. In: Proceedings of the 2nd Conference on Computational Molecular Biology (RECOMB\u201998), pp. 61\u201362 (1998) and in: Proceedings of the 30th Annual ACM Symposium on Theory of Computing (STOC\u201998), pp. 597\u2013603 (1998)","key":"47_CR7","DOI":"10.1089\/cmb.1998.5.423"},{"key":"47_CR8","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1007\/11561071_39","volume-title":"Algorithms \u2013 ESA 2005","author":"M. Crochemore","year":"2005","unstructured":"Crochemore, M., et al.: Approximating the 2-interval pattern problem. In: Brodal, G.S., Leonardi, S. (eds.) ESA 2005. LNCS, vol.\u00a03669, pp. 426\u2013437. Springer, Heidelberg (2005)"},{"unstructured":"Deogun, J.S., et al.: RNA secondary structure prediction with simple pseudoknots. In: Proceedings of the 2nd Asia-Pacific Bioinformatics Conference (APBC\u201904), pp. 239\u2013246 (2004)","key":"47_CR9"},{"issue":"6","key":"47_CR10","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1021\/bi00327a032","volume":"24","author":"K.A. Dill","year":"1985","unstructured":"Dill, K.A.: Theory for the folding and stability of globular proteins. Biochemistry\u00a024(6), 1501\u20131509 (1985)","journal-title":"Biochemistry"},{"key":"47_CR11","doi-asserted-by":"publisher","first-page":"7133","DOI":"10.1021\/bi00483a001","volume":"29","author":"K.A. Dill","year":"1990","unstructured":"Dill, K.A.: Dominant forces in protein folding. Biochemistry\u00a029, 7133\u20137155 (1990)","journal-title":"Biochemistry"},{"issue":"11","key":"47_CR12","doi-asserted-by":"publisher","first-page":"1457","DOI":"10.1038\/nbt1104-1457","volume":"22","author":"S.R. Eddy","year":"2004","unstructured":"Eddy, S.R.: How do RNA folding algorithms work? Nature Biotechnology\u00a022(11), 1457\u20131458 (2004)","journal-title":"Nature Biotechnology"},{"issue":"1","key":"47_CR13","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1006\/jmbi.1995.0356","volume":"250","author":"A.P. Gultyaev","year":"1995","unstructured":"Gultyaev, A.P., van Batenburg, F.H.D., Pleij, C.W.A.: The computer simulation of RNA folding pathways using a genetic algorithm. Journal of Molecular Biology\u00a0250(1), 37\u201351 (1995)","journal-title":"Journal of Molecular Biology"},{"doi-asserted-by":"crossref","unstructured":"Hart, W.E., Istrail, S.: Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal. In: Proc. 27th Annual ACM Symposium on Theory of Computing (STOC\u201995), pp. 157\u2013168 (1995)","key":"47_CR14","DOI":"10.1145\/225058.225106"},{"issue":"2","key":"47_CR15","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/BF00818163","volume":"125","author":"I.L. Hofacker","year":"1994","unstructured":"Hofacker, I.L., et al.: Fast folding and comparison of RNA secondary structures. Monatshefte f\u00fcr Chemie\u00a0125(2), 167\u2013188 (1994)","journal-title":"Monatshefte f\u00fcr Chemie"},{"issue":"6","key":"47_CR16","doi-asserted-by":"publisher","first-page":"981","DOI":"10.1089\/106652703322756186","volume":"10","author":"S. Ieong","year":"2003","unstructured":"Ieong, S., et al.: Predicting RNA secondary structure with arbitrary pseudoknots by maximizing the number of stacking pairs. Journal of Computational Biology\u00a010(6), 981\u2013995 (2003)","journal-title":"Journal of Computational Biology"},{"unstructured":"Jiang, M.: A 2-approximation for the preceding-and-crossing structured 2-interval pattern problem. Journal of Combinatorial Optimization, Special Issue on Bioinformatics, to appear","key":"47_CR17"},{"key":"47_CR18","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1007\/978-3-540-72870-2_38","volume-title":"Algorithmic Aspects in Information and Management","author":"M. Jiang","year":"2007","unstructured":"Jiang, M.: Improved approximation algorithms for predicting RNA secondary structures with arbitrary pseudoknots. In: Kao, M.-Y., Li, X.-Y. (eds.) AAIM 2007. LNCS, vol.\u00a04508, pp. 399\u2013410. Springer, Heidelberg (2007)"},{"issue":"1","key":"47_CR19","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1142\/S0219720005000850","volume":"3","author":"M. Jiang","year":"2005","unstructured":"Jiang, M., Zhu, B.: Protein folding on the hexagonal lattice in the HP model. Journal of Bioinformatics and Computational Biology\u00a03(1), 19\u201334 (2005)","journal-title":"Journal of Bioinformatics and Computational Biology"},{"issue":"4598","key":"47_CR20","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1126\/science.220.4598.671","volume":"220","author":"S. Kirkpatrick","year":"1983","unstructured":"Kirkpatrick, S., Gelatt Jr., C.D., Vecchi, M.P.: Optimization by simulated annealing. Science\u00a0220(4598), 671\u2013680 (1983)","journal-title":"Science"},{"doi-asserted-by":"crossref","unstructured":"Lesh, N., Mitzenmacher, M., Whiteslides, S.: A complete and effective move set for simplified protein folding. In: Proceedings of the 7th Annual International Conference on Computational Molecular Biology (RECOMB\u201903), pp. 188\u2013195 (2003)","key":"47_CR21","DOI":"10.1145\/640075.640099"},{"key":"47_CR22","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1007\/978-3-540-27836-8_77","volume-title":"Automata, Languages and Programming","author":"R.B. Lyngs\u00f8","year":"2004","unstructured":"Lyngs\u00f8, R.B.: Complexity of pseudoknot prediction in simple models. In: D\u00edaz, J., et al. (eds.) ICALP 2004. LNCS, vol.\u00a03142, pp. 919\u2013931. Springer, Heidelberg (2004)"},{"issue":"3-4","key":"47_CR23","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1089\/106652700750050862","volume":"7","author":"R.B. Lyngs\u00f8","year":"2000","unstructured":"Lyngs\u00f8, R.B., Pedersen, C.N.S.: RNA pseudoknot prediction in energy-based models. Journal of Computational Biology\u00a07(3-4), 409\u2013427 (2000)","journal-title":"Journal of Computational Biology"},{"issue":"6","key":"47_CR24","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1093\/bioinformatics\/15.6.440","volume":"15","author":"R.B. Lyngs\u00f8","year":"1999","unstructured":"Lyngs\u00f8, R.B., Zuker, M., Pedersen, C.N.S.: Fast evaluation of interval loops in RNA secondary structure prediction. Bioinformatics\u00a015(6), 440\u2013445 (1999)","journal-title":"Bioinformatics"},{"unstructured":"Mauri, G., Pavesi, G., Piccolboni, A.: Approximation algorithms for protein folding prediction. In: Proceedings of the 10th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA\u201999), pp. 945\u2013946 (1999)","key":"47_CR25"},{"unstructured":"Newman, A.: A new algorithm for protein folding in the HP model. In: Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA\u201902), pp. 876\u2013884 (2002)","key":"47_CR26"},{"issue":"1","key":"47_CR27","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1137\/0135006","volume":"35","author":"R. Nussinov","year":"1978","unstructured":"Nussinov, R., et al.: Algorithms for loop matching. SIAM Journal on Applied Mathematics\u00a035(1), 68\u201382 (1978)","journal-title":"SIAM Journal on Applied Mathematics"},{"key":"47_CR28","doi-asserted-by":"publisher","first-page":"2053","DOI":"10.1006\/jmbi.1998.2436","volume":"285","author":"E. Rivas","year":"1999","unstructured":"Rivas, E., Eddy, S.R.: A dynamic programming algorithm for RNA structure prediction including pseudoknots. Journal of Molecular Biology\u00a0285, 2053\u20132068 (1999)","journal-title":"Journal of Molecular Biology"},{"issue":"1","key":"47_CR29","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1093\/bioinformatics\/btg373","volume":"20","author":"J. Ruan","year":"2004","unstructured":"Ruan, J., Stormo, G.D., Zhang, W.: An iterated loop matching approach to the prediction of RNA secondary structure with pseudoknots. Bioinformatics\u00a020(1), 58\u201366 (2004)","journal-title":"Bioinformatics"},{"issue":"4","key":"47_CR30","first-page":"459","volume":"13","author":"B.A. Shapiro","year":"1997","unstructured":"Shapiro, B.A., Wu, J.C.: Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm. Computer Applications in the Biosciences\u00a013(4), 459\u2013471 (1997)","journal-title":"Computer Applications in the Biosciences"},{"issue":"8","key":"47_CR31","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1093\/bioinformatics\/14.8.691","volume":"14","author":"J.E. Tabaska","year":"1998","unstructured":"Tabaska, J.E., et al.: An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics\u00a014(8), 691\u2013699 (1998)","journal-title":"Bioinformatics"},{"key":"47_CR32","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1038\/newbio246040a0","volume":"246","author":"I. Tinoco","year":"1973","unstructured":"Tinoco, I., et al.: Improved estimation of secondary structure in ribonucleic acids. Nature New Biology\u00a0246, 40\u201342 (1973)","journal-title":"Nature New Biology"},{"issue":"2","key":"47_CR33","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1016\/S0304-3975(98)00090-5","volume":"210","author":"Y. Uemura","year":"1999","unstructured":"Uemura, Y., et al.: Tree adjoining grammars for RNA structure prediction. Theoretical Computer Science\u00a0210(2), 277\u2013303 (1999)","journal-title":"Theoretical Computer Science"},{"key":"47_CR34","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1016\/j.tcs.2003.08.010","volume":"312","author":"S. Vialette","year":"2004","unstructured":"Vialette, S.: On the computational complexity of 2-interval pattern matching problems. Theoretical Computer Science\u00a0312, 223\u2013249 (2004)","journal-title":"Theoretical Computer Science"},{"key":"47_CR35","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-6846-3","volume-title":"Introduction to Computational Biology: Maps, Sequences and Genomes","author":"M.S. Waterman","year":"1995","unstructured":"Waterman, M.S.: Introduction to Computational Biology: Maps, Sequences and Genomes. Chapman and Hall, Boca Raton (1995)"},{"issue":"1","key":"47_CR36","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1093\/nar\/9.1.133","volume":"9","author":"M. Zuker","year":"1981","unstructured":"Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research\u00a09(1), 133\u2013148 (1981)","journal-title":"Nucleic Acids Research"}],"container-title":["Lecture Notes in Computer Science","Bioinformatics Research and Applications"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-72031-7_47.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,19]],"date-time":"2020-11-19T05:28:12Z","timestamp":1605763692000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-72031-7_47"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[null]]},"ISBN":["9783540720300","9783540720317"],"references-count":36,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-72031-7_47","relation":{},"subject":[]}}