{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,6]],"date-time":"2025-12-06T17:05:16Z","timestamp":1765040716469},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"S4","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2017,9]]},"DOI":"10.1186\/s12918-017-0459-4","type":"journal-article","created":{"date-parts":[[2017,9,21]],"date-time":"2017-09-21T07:38:34Z","timestamp":1505979514000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Hybrid method to solve HP model on 3D lattice and to probe protein stability upon amino acid mutations"],"prefix":"10.1186","volume":"11","author":[{"given":"Yuzhen","family":"Guo","sequence":"first","affiliation":[]},{"given":"Fengying","family":"Tao","sequence":"additional","affiliation":[]},{"given":"Zikai","family":"Wu","sequence":"additional","affiliation":[]},{"given":"Yong","family":"Wang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,9,21]]},"reference":[{"issue":"4","key":"459_CR1","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1002\/pro.5560040401","volume":"4","author":"KA Dill","year":"1995","unstructured":"Dill KA, Bromberg S, Yue K, et al. Principles of protein folding a perspective from simple exact models. Protein Sci. 1995; 4(4):561\u2013602.","journal-title":"Protein Sci"},{"issue":"1","key":"459_CR2","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1049\/iet-syb.2015.0059","volume":"10","author":"YZ Guo","year":"2016","unstructured":"Guo YZ, Wu Z, Wang Y, et al. Extended particle swarm optimization method for folding protein on triangular lattice. IET Sys Bio. 2016; 10(1):30\u201333.","journal-title":"IET Sys Bio"},{"issue":"22","key":"459_CR3","first-page":"1320","volume":"18","author":"M Nardelli","year":"2013","unstructured":"Nardelli M, Tedesco L, Bechini A. Cross-lattice Behavior of General ACO Folding for Proteins in the HP Model. Proc of the 28th Annual ACM Symp on Appl Comput. 2013; 18(22):1320\u20131327.","journal-title":"Proc of the 28th Annual ACM Symp on Appl Comput"},{"issue":"1","key":"459_CR4","first-page":"19","volume":"1","author":"Y Zhang","year":"2012","unstructured":"Zhang Y, Wu L. Artificial Bee Colony for Two Dimensional Protein Folding. Adv Electr Eng Syst. 2012; 1(1):19\u201323.","journal-title":"Adv Electr Eng Syst"},{"issue":"02","key":"459_CR5","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1142\/S0219720005001107","volume":"3","author":"XS Zhang","year":"2005","unstructured":"Zhang XS, Wang Y, Zhan ZW, Wu LY, Chen LN. Exploring protein\u2019s optimal HP configurations by self-organizing mapping. J Bioinf Comput Biol. 2005; 3(02):385\u2013400.","journal-title":"J Bioinf Comput Biol"},{"issue":"3","key":"459_CR6","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1007\/s10910-014-0459-1","volume":"53","author":"JM Garc\u00eda-Mart\u00ednez","year":"2015","unstructured":"Garc\u00eda-Mart\u00ednez JM, Garz\u00f3n EM, Cecilia JM, et al. An efficient approach for solving the HP protein folding problem based on UEGO. J Math Chem. 2015; 53(3):794\u2013806.","journal-title":"J Math Chem"},{"key":"459_CR7","first-page":"140","volume":"13","author":"CJ Lin","year":"2011","unstructured":"Lin CJ, Su SC. Protein 3D HP model folding simulation using a hybrid of genetic algorithm and particle swarm optimization. Int J Fuzzy Syst. 2011; 13:140\u2013147.","journal-title":"Int J Fuzzy Syst"},{"key":"459_CR8","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1007\/s13173-010-0002-6","volume":"16","author":"CMV Ben\u00edtez","year":"2010","unstructured":"Ben\u00edtez CMV, Lopes HS. Protein structure prediction with the 3D-HP side-chain model using a master-slave parallel genetic algorithm. J Braz Comput Soc. 2010; 16:69\u201378.","journal-title":"J Braz Comput Soc"},{"issue":"1","key":"459_CR9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1477-5956-11-1","volume":"11","author":"JJ Tsay","year":"2013","unstructured":"Tsay JJ, Su SC. An effective evolutionary algorithm for protein folding on 3D FCC HP model by lattice rotation and generalized move sets. Proteome Sci. 2013; 11(1):1.","journal-title":"Proteome Sci"},{"key":"459_CR10","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1109\/MHS.1995.494215","volume":"1","author":"RC Eberhart","year":"1995","unstructured":"Eberhart RC, Kennedy J. A new optimizer using particle swarm theory. Proc of the sixth Int Symp on micro Mach Hum Sci. 1995; 1:39\u201343.","journal-title":"Proc of the sixth Int Symp on micro Mach Hum Sci"},{"issue":"4096","key":"459_CR11","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.181.4096.223","volume":"181","author":"CB Anfinsen","year":"1973","unstructured":"Anfinsen CB. Principles that govern the folding of protein chains. Sci. 1973; 181(4096):223\u2013230.","journal-title":"Sci"},{"issue":"3","key":"459_CR12","first-page":"190","volume":"1","author":"F Glover","year":"1989","unstructured":"Glover F. Tabu search-part I. J Comput. 1989; 1(3):190\u2013206.","journal-title":"J Comput"},{"issue":"23","key":"459_CR13","doi-asserted-by":"crossref","first-page":"234703","DOI":"10.1063\/1.2402162","volume":"125","author":"YZ Guo","year":"2006","unstructured":"Guo YZ, Feng EM. The simulation of the three-dimensional lattice hydrophobic-polar protein folding. J Chem Phys. 2006; 125(23):234703.","journal-title":"J Chem Phys"},{"key":"459_CR14","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.compbiolchem.2012.02.001","volume":"28","author":"J Liu","year":"2012","unstructured":"Liu J, Li G, Yu J, et al. Heuristic energy landscape paving for protein folding problem in the three-dimensional HP lattice model. Comput Biol Chem. 2012; 28:17\u201326.","journal-title":"Comput Biol Chem"},{"issue":"6327","key":"459_CR15","first-page":"812","volume":"355","author":"L Pascal","year":"2017","unstructured":"Pascal L, Stefan G, Abdullah K, Valentina C, Paul JB, Christian M, Mering C, Paola P. Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability. Science. 2017; 355(6327):812.","journal-title":"Science"},{"issue":"suppl 2","key":"459_CR16","doi-asserted-by":"crossref","first-page":"W239","DOI":"10.1093\/nar\/gkl190","volume":"34","author":"V Parthiban","year":"2006","unstructured":"Parthiban V, Michael MG, Schomburg D. CUPSAT: prediction of protein stability upon point mutation. Nucleic Acids Res. 2006; 34(suppl 2):W239-W242.","journal-title":"Nucleic Acids Res"},{"key":"459_CR17","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1002\/prot.20810","volume":"62","author":"J Cheng","year":"2006","unstructured":"Cheng J, Randall A, Baldi P. Prediction of Protein Stability Changes for Single Site Mutations Using Support Vector Machines, Proteins: Str. Func Bioi. 2006; 62:1125\u201332.","journal-title":"Func Bioi"},{"key":"459_CR18","doi-asserted-by":"crossref","first-page":"8033","DOI":"10.1021\/bi00487a007","volume":"29","author":"D Shortle","year":"1990","unstructured":"Shortle D, Stites WE, Meeker AK. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochem. 1990; 29:8033\u201341.","journal-title":"Biochem"},{"issue":"5","key":"459_CR19","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/75151","volume":"7","author":"D Perl","year":"2000","unstructured":"Perl D, Mueller U, Heinemann U, Schmid FX. Two exposed amino acid residues confer thermostability on a cold shock protein. Nat Struct Bio. 2000; 7(5):380\u20133.","journal-title":"Nat Struct Bio"},{"issue":"10","key":"459_CR20","doi-asserted-by":"crossref","first-page":"2166","DOI":"10.1002\/pro.5560061011","volume":"6","author":"DW Miller","year":"1997","unstructured":"Miller DW, Dill KA. Ligand binding to proteins: The binding landscape model. Prot Sci. 1997; 6(10):2166\u201379.","journal-title":"Prot Sci"},{"issue":"4","key":"459_CR21","doi-asserted-by":"crossref","first-page":"1935","DOI":"10.1063\/1.1383051","volume":"115","author":"BP Blackburne","year":"2001","unstructured":"Blackburne BP, Hirst JD. Evolution of functional model proteins. J Chem Phys. 2001; 115(4):1935\u201342.","journal-title":"J Chem Phys"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-017-0459-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,9,21]],"date-time":"2017-09-21T07:41:06Z","timestamp":1505979666000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-017-0459-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,9]]},"references-count":21,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2017,9]]}},"alternative-id":["459"],"URL":"https:\/\/doi.org\/10.1186\/s12918-017-0459-4","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,9]]},"article-number":"93"}}