{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,4]],"date-time":"2022-04-04T11:03:22Z","timestamp":1649070202646},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"S2","license":[{"start":{"date-parts":[[2013,1,1]],"date-time":"2013-01-01T00:00:00Z","timestamp":1356998400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,1]]},"DOI":"10.1186\/1471-2105-14-s2-s16","type":"journal-article","created":{"date-parts":[[2013,1,21]],"date-time":"2013-01-21T15:16:12Z","timestamp":1358781372000},"source":"Crossref","is-referenced-by-count":11,"title":["Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice"],"prefix":"10.1186","volume":"14","author":[{"given":"Mahmood A","family":"Rashid","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"MA Hakim","family":"Newton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Md Tamjidul","family":"Hoque","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Swakkhar","family":"Shatabda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Duc Nghia","family":"Pham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abdul","family":"Sattar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,1,21]]},"reference":[{"issue":"6968","key":"5605_CR1","first-page":"78","volume":"426","author":"Adam Smith","year":"2003","unstructured":"Smith Adam: Protein misfolding. Nature Reviews Drug Discovery. 2003, 426 (6968): 78-102.","journal-title":"Nature Reviews Drug Discovery"},{"issue":"6968","key":"5605_CR2","doi-asserted-by":"publisher","first-page":"884","DOI":"10.1038\/nature02261","volume":"426","author":"CM Dobso","year":"2003","unstructured":"Dobso CM: Protein folding and misfolding. Nature. 2003, 426 (6968): 884-890. 10.1038\/nature02261.","journal-title":"Nature"},{"issue":"5731","key":"5605_CR3","first-page":"78","volume":"309","author":"The Science Editorial","year":"2005","unstructured":"The Science Editorial: So much more to know. The Science. 2005, 309 (5731): 78-102.","journal-title":"The Science"},{"key":"5605_CR4","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1146\/annurev.biophys.30.1.173","volume":"30","author":"R Bonneau","year":"2001","unstructured":"Bonneau R, Baker D: Ab initio protein structure prediction: progress and prospects. Annual Review of Biophysics and Biomolecular Structure. 2001, 30: 173-89. 10.1146\/annurev.biophys.30.1.173.","journal-title":"Annual Review of Biophysics and Biomolecular Structure"},{"key":"5605_CR5","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/S0076-6879(04)83004-0","volume":"383","author":"C Rohl","year":"2004","unstructured":"Rohl C, Strauss C, Misura K, Baker D: Protein structure prediction using ROSETTA. Methods in Enzymology. 2004, 383: 66-93.","journal-title":"Methods in Enzymology"},{"key":"5605_CR6","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/978-1-4020-9058-5_1","volume-title":"From Protein Structure to Function with Bioinformatics","author":"J Lee","year":"2009","unstructured":"Lee J, Wu S, Zhang Y: Ab initio protein structure prediction. From Protein Structure to Function with Bioinformatics. 2009, 3-25."},{"key":"5605_CR7","volume-title":"Journal of Molecular Biology","author":"Y Xia","year":"2008","unstructured":"Xia Y, Huang ES, Levitt M, Samudrala R: Ab initio construction of protein tertiary structures using a hierarchical approach. Journal of Molecular Biology. 2008"},{"key":"5605_CR8","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1145\/2382936.2382980","volume-title":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","author":"S Shatabda","year":"2012","unstructured":"Shatabda S, Newton M, Pham DN, Sattar A: Memorybased local search for simplified protein structure prediction. Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2012, ACM, 345-352."},{"key":"5605_CR9","first-page":"241","volume":"1","author":"M Cebri\u00e1n","year":"2008","unstructured":"Cebri\u00e1n M, Dot\u00fa I, Van Hentenryck P, Clote P: Protein structure prediction on the face centered cubic lattice by local search. Proceedings of the Conference on Artificial Intelligence. 2008, 1: 241-246.","journal-title":"Proceedings of the Conference on Artificial Intelligence"},{"key":"5605_CR10","volume-title":"IEEE Transactions on Computational Biology and Bioinformatics","author":"I Dotu","year":"2011","unstructured":"Dotu I, Cebri\u00e1n M, Van Hentenryck P, Clote P: On lattice protein structure prediction revisited. IEEE Transactions on Computational Biology and Bioinformatics. 2011"},{"key":"5605_CR11","first-page":"4138","volume-title":"IEEE Transactions on Computational Biology and Bioinformatics","author":"MT Hoque","year":"2007","unstructured":"Hoque MT, Chetty M, Sattar A: Protein folding prediction in 3D FCC HP lattice model using genetic algorithm. IEEE Transactions on Computational Biology and Bioinformatics. 2007, IEEE Congress on Evolutionary Computation, 2007: 4138-4145."},{"key":"5605_CR12","first-page":"369","volume-title":"WABI","author":"HJ B\u00f6ckenhauer","year":"2008","unstructured":"B\u00f6ckenhauer HJ, Ullah AZMD, Kapsokalivas L, Steinh\u00f6fel K: A local move set for protein folding in triangular lattice models. WABI. 2008, Lecture Notes in Computer Science, Springer, 5251: 369-381."},{"key":"5605_CR13","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1145\/2382936.2383043","volume-title":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","author":"MA Rashid","year":"2012","unstructured":"Rashid MA, Shatabda S, Newton M, Hoque MT, Pham DN, Sattar A: Random-walk: a stagnation recovery technique for simplified protein structure prediction. Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2012, ACM, 620-622."},{"key":"5605_CR14","first-page":"44","volume":"65","author":"C Levinthal","year":"1968","unstructured":"Levinthal C: Are there pathways for protein folding?. Journal of Medical Physics. 1968, 65: 44-45.","journal-title":"Journal of Medical Physics"},{"issue":"4096","key":"5605_CR15","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1126\/science.181.4096.223","volume":"181","author":"CB Anfinsen","year":"1973","unstructured":"Anfinsen CB: The principles that govern the folding of protein chains. Science. 1973, 181 (4096): 223-230. 10.1126\/science.181.4096.223.","journal-title":"Science"},{"key":"5605_CR16","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1089\/cmb.1998.5.27","volume":"5","author":"B Berger","year":"1998","unstructured":"Berger B, Leightont T: Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete. Journal of Computational Biology. 1998, 5: 27-40. 10.1089\/cmb.1998.5.27.","journal-title":"Journal of Computational Biology"},{"key":"5605_CR17","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1073\/pnas.92.1.325","volume":"92","author":"K Yue","year":"1995","unstructured":"Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI, Dill KA: A test of lattice protein folding algorithms. Proceedings of the National Academy of Sciences of the United States of America. 1995, 92: 325-10.1073\/pnas.92.1.325.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"5605_CR18","volume-title":"Tabu search","author":"F Glover","year":"1998","unstructured":"Glover F, Laguna M: Tabu search. 1998, Kluwer Academic Pub, 1:"},{"issue":"3","key":"5605_CR19","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1287\/ijoc.1.3.190","volume":"1","author":"F Glover","year":"1989","unstructured":"Glover F: Tabu search - part I. ORSA Journal on Computing. 1989, 1 (3): 190-206. 10.1287\/ijoc.1.3.190.","journal-title":"ORSA Journal on Computing"},{"issue":"3","key":"5605_CR20","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.4007\/annals.2005.162.1065","volume":"162","author":"T Hales","year":"2005","unstructured":"Hales T: A proof of the kepler conjecture. The Annals of Mathematics. 2005, 162 (3): 1065-1185. 10.4007\/annals.2005.162.1065.","journal-title":"The Annals of Mathematics"},{"issue":"6","key":"5605_CR21","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1021\/bi00327a032","volume":"24","author":"KA Dill","year":"1985","unstructured":"Dill KA: Theory for the folding and stability of globular proteins. Biochemistry. 1985, 24 (6): 1501-1509. 10.1021\/bi00327a032.","journal-title":"Biochemistry"},{"issue":"10","key":"5605_CR22","doi-asserted-by":"publisher","first-page":"3986","DOI":"10.1021\/ma00200a030","volume":"22","author":"KF Lau","year":"1989","unstructured":"Lau KF, Dill KA: A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules. 1989, 22 (10): 3986-3997. 10.1021\/ma00200a030.","journal-title":"Macromolecules"},{"key":"5605_CR23","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1186\/1471-2105-8-342","volume":"8","author":"C Thachuk","year":"2007","unstructured":"Thachuk C, Shmygelska A, Hoos HH: A replica exchange monte carlo algorithm for protein folding in the HP model. BMC Bioinformatics. 2007, 8: 342-10.1186\/1471-2105-8-342.","journal-title":"BMC Bioinformatics"},{"key":"5605_CR24","volume-title":"Soft Computing - A Fusion of Foundations, Methodologies and Applications","author":"AA Tantar","year":"2008","unstructured":"Tantar AA, Melab N, Talbi EG: A grid-based genetic algorithm combined with an adaptive simulated annealing for protein structure prediction. Soft Computing - A Fusion of Foundations, Methodologies and Applications. 2008"},{"key":"5605_CR25","first-page":"581","volume-title":"Soft Computing - A Fusion of Foundations, Methodologies and Applications","author":"R Unger","year":"1993","unstructured":"Unger R, Moult J: A genetic algorithm for 3D protein folding simulations. Soft Computing - A Fusion of Foundations, Methodologies and Applications. 1993, Morgan Kaufmann Publishers, The 5th International Conference on Genetic Algorithms, 581-"},{"key":"5605_CR26","volume-title":"PhD thesis","author":"MT Hoque","year":"2007","unstructured":"Hoque MT: Genetic algorithm for ab initio protein structure prediction based on low resolution models. PhD thesis. 2007, Gippsland School of Information Technology, Monash University, Australia"},{"key":"5605_CR27","volume-title":"Proceedings of the Conference on Artificial Intelligence","author":"GW Klau","year":"2002","unstructured":"Klau GW, Lesh N, Marks J, Mitzenmacher M: Humanguided tabu search. Proceedings of the Conference on Artificial Intelligence. 2002"},{"issue":"4","key":"5605_CR28","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1016\/j.plrev.2005.10.001","volume":"2","author":"C Blum","year":"2005","unstructured":"Blum C: Ant colony optimization: introduction and recent trends. Physics of Life Reviews. 2005, 2 (4): 353-373. 10.1016\/j.plrev.2005.10.001.","journal-title":"Physics of Life Reviews"},{"key":"5605_CR29","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1109\/TEVC.2006.880328","volume":"11","author":"V Cutello","year":"2007","unstructured":"Cutello V, Nicosia G, Pavone M, Timmis J: An immune algorithm for protein structure prediction on lattice models. IEEE Transaction on Evolutionary Computing. 2007, 11: 101-117.","journal-title":"IEEE Transaction on Evolutionary Computing"},{"key":"5605_CR30","volume-title":"IEEE Transaction on Evolutionary Computing","author":"AL Patton","year":"1995","unstructured":"Patton AL, Punch WF III, Goodman ED: A standard GA approach to native protein conformation prediction. IEEE Transaction on Evolutionary Computing. 1995, International Conference on Genetic Algorithms"},{"issue":"13-15","key":"5605_CR31","doi-asserted-by":"publisher","first-page":"2308","DOI":"10.1016\/j.neucom.2010.02.021","volume":"73","author":"MT Hoque","year":"2010","unstructured":"Hoque MT, Chetty M, Lewis A, Sattar A, Avery VM: DFS-generated pathways in GA crossover for protein structure prediction. Neurocomputing. 2010, 73 (13-15): 2308-2316. 10.1016\/j.neucom.2010.02.021.","journal-title":"Neurocomputing"},{"key":"5605_CR32","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1109\/TCBB.2009.34","volume":"8","author":"MT Hoque","year":"2011","unstructured":"Hoque MT, Chetty M, Lewis A, Sattar A: Twin removal in genetic algorithms for protein structure prediction using low-resolutionmodel. IEEE Transactions on Computational Biology and Bioinformatics. 2011, 8: 234-245.","journal-title":"IEEE Transactions on Computational Biology and Bioinformatics"},{"issue":"3","key":"5605_CR33","doi-asserted-by":"publisher","first-page":"2267","DOI":"10.1103\/PhysRevE.48.2267","volume":"48","author":"K Yue","year":"1993","unstructured":"Yue K, Dill KA: Sequence-structure relationships in proteins and copolymers. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993, 48 (3): 2267-2278. 10.1103\/PhysRevE.48.2267.","journal-title":"Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics"},{"key":"5605_CR34","first-page":"188","volume-title":"Research in Computational Molecular Biology (RECOMB)","author":"N Lesh","year":"2003","unstructured":"Lesh N, Mitzenmacher M, Whitesides S: A complete and effective move set for simplified protein folding. Research in Computational Molecular Biology (RECOMB). 2003, 188-195."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S2-S16.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-S2-S16\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S2-S16.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T10:19:16Z","timestamp":1548152356000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S2-S16"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1]]},"references-count":34,"journal-issue":{"issue":"S2","published-print":{"date-parts":[[2013,1]]}},"alternative-id":["5605"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s2-s16","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,1]]},"article-number":"S16"}}