Three-dimensional protein structure prediction based on memetic algorithms
•An algorithm to deal with the 3-D protein structure prediction problem is proposed.•The method is a multimodal evolutionary algorithm allied to a local search strategy.•The method was built as an incremental approach based on promising evolutionary components.•Results are topologically compatible w...
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| Veröffentlicht in: | Computers & operations research Jg. 91; S. 160 - 177 |
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01.03.2018
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| ISSN: | 0305-0548, 1873-765X, 0305-0548 |
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| Abstract | •An algorithm to deal with the 3-D protein structure prediction problem is proposed.•The method is a multimodal evolutionary algorithm allied to a local search strategy.•The method was built as an incremental approach based on promising evolutionary components.•Results are topologically compatible with the experimentally determined structures.
[Display omitted]
Tertiary protein structure prediction is a challenging problem in Structural Bioinformatics and is classified according to the computational complexity theory as a NP-hard problem. In this paper, we proposed a first-principle method that makes use of a priori information about known protein structures to tackle the three-dimensional protein structure prediction problem. We do so by designing a multimodal memetic algorithm that uses an evolutionary approach with a ternary tree-structured population allied to a local search strategy. The method has been developed based on an incremental approach using the combination of promising evolutionary components to address the concerned multimodal problem. Three memetic algorithms focused on the problem are proposed. The first one modifies a basic version of a memetic algorithm by introducing modified global search operators. The second uses a different population structure for the memetic algorithm. And finally, the last algorithm consists of the integration of global operators and multimodal strategies to deal with the inherent multimodality of the protein structure prediction problem. The implementations take advantage of structural knowledge stored in the Protein Data Bank to guide the exploiting and restrict the protein conformational search space. Predicted three-dimensional protein structures were analyzed regarding root mean square deviation and the global distance total score test. Obtained results for the three versions outperformed the basic version of the memetic algorithm. The third algorithm overcomes the results of the previous two, demonstrating the importance of adapting the method to deal with the complexities of the problem. In addition, the achieved results are topologically compatible with the experimental correspondent, confirming the promising performance of our approach. |
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| AbstractList | Tertiary protein structure prediction is a challenging problem in Structural Bioinformatics and is classified according to the computational complexity theory as a NP-hard problem. In this paper, we proposed a first-principle method that makes use of a priori information about known protein structures to tackle the three-dimensional protein structure prediction problem. We do so by designing a multimodal memetic algorithm that uses an evolutionary approach with a ternary tree-structured population allied to a local search strategy. The method has been developed based on an incremental approach using the combination of promising evolutionary components to address the concerned multimodal problem. Three memetic algorithms focused on the problem are proposed. The first one modifies a basic version of a memetic algorithm by introducing modified global search operators. The second uses a different population structure for the memetic algorithm. And finally, the last algorithm consists of the integration of global operators and multimodal strategies to deal with the inherent multimodality of the protein structure prediction problem. The implementations take advantage of structural knowledge stored in the Protein Data Bank to guide the exploiting and restrict the protein conformational search space. Predicted three-dimensional protein structures were analyzed regarding root mean square deviation and the global distance total score test. Obtained results for the three versions outperformed the basic version of the memetic algorithm. The third algorithm overcomes the results of the previous two, demonstrating the importance of adapting the method to deal with the complexities of the problem. In addition, the achieved results are topologically compatible with the experimental correspondent, confirming the promising performance of our approach. •An algorithm to deal with the 3-D protein structure prediction problem is proposed.•The method is a multimodal evolutionary algorithm allied to a local search strategy.•The method was built as an incremental approach based on promising evolutionary components.•Results are topologically compatible with the experimentally determined structures. [Display omitted] Tertiary protein structure prediction is a challenging problem in Structural Bioinformatics and is classified according to the computational complexity theory as a NP-hard problem. In this paper, we proposed a first-principle method that makes use of a priori information about known protein structures to tackle the three-dimensional protein structure prediction problem. We do so by designing a multimodal memetic algorithm that uses an evolutionary approach with a ternary tree-structured population allied to a local search strategy. The method has been developed based on an incremental approach using the combination of promising evolutionary components to address the concerned multimodal problem. Three memetic algorithms focused on the problem are proposed. The first one modifies a basic version of a memetic algorithm by introducing modified global search operators. The second uses a different population structure for the memetic algorithm. And finally, the last algorithm consists of the integration of global operators and multimodal strategies to deal with the inherent multimodality of the protein structure prediction problem. The implementations take advantage of structural knowledge stored in the Protein Data Bank to guide the exploiting and restrict the protein conformational search space. Predicted three-dimensional protein structures were analyzed regarding root mean square deviation and the global distance total score test. Obtained results for the three versions outperformed the basic version of the memetic algorithm. The third algorithm overcomes the results of the previous two, demonstrating the importance of adapting the method to deal with the complexities of the problem. In addition, the achieved results are topologically compatible with the experimental correspondent, confirming the promising performance of our approach. |
| Author | Borguesan, Bruno Dorn, Márcio Krause, Mathias J. Corrêa, Leonardo de Lima |
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| CitedBy_id | crossref_primary_10_1016_j_pbiomolbio_2019_09_004 crossref_primary_10_1007_s10462_022_10350_x crossref_primary_10_1002_jcc_27112 crossref_primary_10_1016_j_ins_2020_06_003 crossref_primary_10_1016_j_swevo_2022_101062 crossref_primary_10_1016_j_compbiolchem_2022_107773 crossref_primary_10_1016_j_eswa_2021_115018 crossref_primary_10_1109_TCBB_2019_2921958 crossref_primary_10_1109_ACCESS_2022_3176945 crossref_primary_10_1186_s12859_019_3259_6 |
| Cites_doi | 10.1109/4235.996017 10.1007/s11030-006-9053-1 10.1007/BF00175357 10.1126/science.181.4096.223 10.1093/nar/28.1.235 10.1002/prot.24930 10.1093/nar/gkl842 10.1089/cmb.2016.0074 10.1287/moor.6.1.19 10.1007/s12039-011-0189-x 10.1093/bioinformatics/btq007 10.1038/nature15393 10.1126/science.1113801 10.1162/evco.2010.18.1.18102 10.1002/prot.340220202 10.1016/S0959-440X(98)80125-5 10.1107/S0907444902003359 10.1137/S0036144594278060 10.1142/S0219720013500170 10.1016/S0076-6879(04)83004-0 10.1109/TEVC.2005.850260 10.1002/prot.22390 10.1016/j.compbiolchem.2015.08.006 10.1016/j.ins.2013.02.041 10.1109/MCI.2010.936309 10.1016/S0959-440X(00)00067-1 10.1002/prot.340210406 10.1002/prot.24065 10.1002/bip.360221211 10.1002/prot.20264 10.1016/j.swevo.2011.05.005 10.1007/s10559-013-9570-8 10.1002/prot.25064 10.1002/prot.24973 10.1038/nrm1126 10.1016/j.compbiolchem.2014.10.001 10.1002/prot.24470 10.1093/nar/gkg571 10.1093/nar/gkh429 10.1016/0022-2836(84)90231-6 10.1016/S0959-440X(00)00063-4 10.1016/j.jmb.2009.07.063 10.1146/annurev.biophys.29.1.291 10.1162/EVCO_a_00176 10.1002/prot.340210302 10.1126/science.1853201 10.1126/science.220.4598.671 10.1186/1472-6807-13-S1-S4 10.1016/j.str.2013.08.005 10.1002/prot.24448 10.1073/pnas.97.19.10383 10.1002/prot.340230109 10.1016/S0022-2836(03)00021-4 10.1134/S0026893308040195 10.1162/evco.1993.1.1.25 10.1093/nar/gkh468 10.1006/jmbi.1997.0959 |
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| Keywords | PSP problem Structural Bioinformatics Multimodal optimization Metaheuristics Hybrid evolutionary algorithms |
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| References | Tai, Bai, Taylor, Lee (bib0067) 2014; 82 Dorn, Buriol, Lamb (bib0021) 2011 Berman, Westbrook, Feng, Gilliland, Bhat, Weissig, Shindyalov, Bourne (bib0004) 2000; 28 Elofsson, Le Grand, Eisenberg (bib0024) 1995; 23 Kabsch, Sander (bib0035) 1983; 22 Kirkpatrick, Gelatt, Vecchi (bib0039) 1983; 220 Shehu, Kavraki, Clementi (bib0061) 2009; 76 Desjarlais, Clarke (bib0020) 1998; 8 Consortium (bib0014) 2015; 526 Kim, Blum, Bradley, Baker (bib0036) 2009; 393 Chaudhury, Lyskov, Gray (bib0011) 2010; 26 Molina, Lozano, Herrera (bib0048) 2010 Glibovets, Gulayeva (bib0027) 2013; 49 Pruitt, Tatusova, Maglott (bib0056) 2007; 35 Song, DiMaio, Wang, Kim, Miles, Brunette, Thompson, Baker (bib0064) 2013; 21 Heinig, Frishman (bib0031) 2004; 32 Moscato (bib0049) 1989 Osguthorpe (bib0055) 2000; 10 Borguesan, Inostroza-Ponta, Dorn (bib0005) 2016; 24 Bowie, Luthy, Eisenberg (bib0008) 1991; 253 Deb, Pratap, Agarwal, Meyarivan (bib0019) 2002; 6 Bradley, Misura, Baker (bib0009) 2005; 309 Handl, Lovell, Knowles (bib0030) 2008 Zhang, Yang, He, Walker, Zhang, Govindarajoo, Virtanen, Xue, Shen, Zhang (bib0073) 2016; 84 Glover (bib0028) 1994; 4 Kinch, Li, Monastyrskyy, Kryshtafovych, Grishin (bib0038) 2016; 84 Moscato, Cotta (bib0050) 2010; 146 Moult, Fidelis, Kryshtafovych, Schwede, Tramontano (bib0051) 2016; 84 Kortemme, Morozov, Baker (bib0040) 2003; 326 Zemla (bib0072) 2003; 31 Borguesan, e Silva, Grisci, Inostroza-Ponta, Dorn (bib0006) 2015; 59 Talbi (bib0068) 2009; 74 Saleh, Olson, Shehu (bib0060) 2013; 13 Dawkins (bib0018) 1976 Rocha, Custódio, Barbosa, Dardenne (bib0058) 2016 Rohl, Strauss, Misura, Baker (bib0059) 2004; 383 Corrêa, Borguesan, Farfan, Inostroza-Ponta, Dorn (bib0015) 2016; PP Anfinsen (bib0001) 1973; 181 Thomsen (bib0070) 2004; 2 Inostroza-Ponta, Farfán, Dorn (bib0033) 2015 Kim, Chivian, Baker (bib0037) 2004; 32 Kuhlman, Baker (bib0043) 2000; 97 Molina, Lozano, García-Martínez, Herrera (bib0047) 2010; 18 Baxevanis, Ouellette (bib0002) 2004; 43 Simons, Kooperberg, Huang, Baker (bib0062) 1997; 268 Chou (bib0013) 1995; 21 Dorn, Inostroza-Ponta, Buriol, Verli (bib0022) 2013 Lazaridis, Karplus (bib0044) 2000; 10 Neumaier (bib0053) 1997; 39 Srinivasan, Rose (bib0065) 1995; 22 Kryshtafovych, Fidelis, Moult (bib0042) 2014; 82 Lobanov, Bogatyreva, Galzitskaya (bib0045) 2008; 42 Garza-Fabre, Kandathil, Handl, Knowles, Lovell (bib0026) 2016; 24 Boussaïd, Lepagnot, Siarry (bib0007) 2013; 237 Hovmöller, Zhou, Ohlson (bib0032) 2002; 58 Richmond (bib0057) 1984; 178 Tang, Li, Suganthan, Yang, Weise (bib0069) 2009 Bryngelson, Onuchic, Socci, Wolynes (bib0010) 1995; 21 Eshelman (bib0025) 1993; 2 Chivian, Robertson, Bonneau, Baker (bib0012) 2003; 44 Krasnogor, Smith (bib0041) 2005; 9 Daggett, Fersht (bib0016) 2003; 4 Solis, Wets (bib0063) 1981; 6 Mühlenbein, Schlierkamp-Voosen (bib0052) 1993; 1 Das, Maity, Qu, Suganthan (bib0017) 2011; 1 Syswerda (bib0066) 1989 Dorn, e Silva, Buriol, Lamb (bib0023) 2014; 53 Martí-Renom, Stuart, Fiser, Sánchez, Melo, Šali (bib0046) 2000; 29 Zhang, Skolnick (bib0074) 2004; 57 Guyeux, Côte, Bahi, Bienia (bib0029) 2014; 12 Belda, Madurga, Tarragó, Llorà, Giralt (bib0003) 2007; 11 Jayaram, Dhingra, Lakhani, Shekhar (bib0034) 2012; 124 Ong, Lim, Chen (bib0054) 2010; 5 Xu, Zhang (bib0071) 2012; 80 Neumaier (10.1016/j.cor.2017.11.015_bib0053) 1997; 39 Pruitt (10.1016/j.cor.2017.11.015_bib0056) 2007; 35 Ong (10.1016/j.cor.2017.11.015_bib0054) 2010; 5 Bradley (10.1016/j.cor.2017.11.015_bib0009) 2005; 309 Eshelman (10.1016/j.cor.2017.11.015_bib0025) 1993; 2 Borguesan (10.1016/j.cor.2017.11.015_bib0006) 2015; 59 Jayaram (10.1016/j.cor.2017.11.015_bib0034) 2012; 124 Chaudhury (10.1016/j.cor.2017.11.015_bib0011) 2010; 26 Anfinsen (10.1016/j.cor.2017.11.015_bib0001) 1973; 181 Kinch (10.1016/j.cor.2017.11.015_bib0038) 2016; 84 Heinig (10.1016/j.cor.2017.11.015_bib0031) 2004; 32 Richmond (10.1016/j.cor.2017.11.015_bib0057) 1984; 178 Kim (10.1016/j.cor.2017.11.015_bib0036) 2009; 393 Osguthorpe (10.1016/j.cor.2017.11.015_bib0055) 2000; 10 Baxevanis (10.1016/j.cor.2017.11.015_bib0002) 2004; 43 Glover (10.1016/j.cor.2017.11.015_bib0028) 1994; 4 Moscato (10.1016/j.cor.2017.11.015_bib0049) 1989 Srinivasan (10.1016/j.cor.2017.11.015_bib0065) 1995; 22 Syswerda (10.1016/j.cor.2017.11.015_bib0066) 1989 Handl (10.1016/j.cor.2017.11.015_bib0030) 2008 Shehu (10.1016/j.cor.2017.11.015_bib0061) 2009; 76 Thomsen (10.1016/j.cor.2017.11.015_bib0070) 2004; 2 Kim (10.1016/j.cor.2017.11.015_sbref0037) 2004; 32 Zhang (10.1016/j.cor.2017.11.015_bib0074) 2004; 57 Desjarlais (10.1016/j.cor.2017.11.015_bib0020) 1998; 8 Garza-Fabre (10.1016/j.cor.2017.11.015_bib0026) 2016; 24 Krasnogor (10.1016/j.cor.2017.11.015_bib0041) 2005; 9 Das (10.1016/j.cor.2017.11.015_bib0017) 2011; 1 Rohl (10.1016/j.cor.2017.11.015_bib0059) 2004; 383 Guyeux (10.1016/j.cor.2017.11.015_bib0029) 2014; 12 Dorn (10.1016/j.cor.2017.11.015_bib0022) 2013 Kryshtafovych (10.1016/j.cor.2017.11.015_bib0042) 2014; 82 Chivian (10.1016/j.cor.2017.11.015_sbref0012) 2003; 44 Martí-Renom (10.1016/j.cor.2017.11.015_bib0046) 2000; 29 Dorn (10.1016/j.cor.2017.11.015_bib0021) 2011 Simons (10.1016/j.cor.2017.11.015_bib0062) 1997; 268 Glibovets (10.1016/j.cor.2017.11.015_bib0027) 2013; 49 Rocha (10.1016/j.cor.2017.11.015_bib0058) 2016 Bryngelson (10.1016/j.cor.2017.11.015_bib0010) 1995; 21 Daggett (10.1016/j.cor.2017.11.015_bib0016) 2003; 4 Dorn (10.1016/j.cor.2017.11.015_bib0023) 2014; 53 Kirkpatrick (10.1016/j.cor.2017.11.015_bib0039) 1983; 220 Saleh (10.1016/j.cor.2017.11.015_bib0060) 2013; 13 Hovmöller (10.1016/j.cor.2017.11.015_bib0032) 2002; 58 Inostroza-Ponta (10.1016/j.cor.2017.11.015_bib0033) 2015 Mühlenbein (10.1016/j.cor.2017.11.015_bib0052) 1993; 1 Xu (10.1016/j.cor.2017.11.015_bib0071) 2012; 80 Consortium (10.1016/j.cor.2017.11.015_bib0014) 2015; 526 Lazaridis (10.1016/j.cor.2017.11.015_bib0044) 2000; 10 Bowie (10.1016/j.cor.2017.11.015_bib0008) 1991; 253 Moscato (10.1016/j.cor.2017.11.015_bib0050) 2010; 146 Belda (10.1016/j.cor.2017.11.015_bib0003) 2007; 11 Kortemme (10.1016/j.cor.2017.11.015_bib0040) 2003; 326 Talbi (10.1016/j.cor.2017.11.015_sbref0068) 2009; 74 Tang (10.1016/j.cor.2017.11.015_bib0069) 2009 Chou (10.1016/j.cor.2017.11.015_bib0013) 1995; 21 Elofsson (10.1016/j.cor.2017.11.015_bib0024) 1995; 23 Tai (10.1016/j.cor.2017.11.015_bib0067) 2014; 82 Moult (10.1016/j.cor.2017.11.015_bib0051) 2016; 84 Dawkins (10.1016/j.cor.2017.11.015_bib0018) 1976 Molina (10.1016/j.cor.2017.11.015_bib0047) 2010; 18 Zhang (10.1016/j.cor.2017.11.015_bib0073) 2016; 84 Deb (10.1016/j.cor.2017.11.015_bib0019) 2002; 6 Borguesan (10.1016/j.cor.2017.11.015_bib0005) 2016; 24 Corrêa (10.1016/j.cor.2017.11.015_sbref0015) 2016; PP Molina (10.1016/j.cor.2017.11.015_bib0048) 2010 Berman (10.1016/j.cor.2017.11.015_bib0004) 2000; 28 Kuhlman (10.1016/j.cor.2017.11.015_bib0043) 2000; 97 Boussaïd (10.1016/j.cor.2017.11.015_bib0007) 2013; 237 Song (10.1016/j.cor.2017.11.015_bib0064) 2013; 21 Lobanov (10.1016/j.cor.2017.11.015_bib0045) 2008; 42 Solis (10.1016/j.cor.2017.11.015_bib0063) 1981; 6 Kabsch (10.1016/j.cor.2017.11.015_bib0035) 1983; 22 Zemla (10.1016/j.cor.2017.11.015_bib0072) 2003; 31 |
| References_xml | – volume: 22 start-page: 81 year: 1995 end-page: 99 ident: bib0065 article-title: Linus: a hierarchic procedure to predict the fold of a protein publication-title: Proteins Struct. Funct. Bioinf. – volume: 309 start-page: 1868 year: 2005 end-page: 1871 ident: bib0009 article-title: Toward high-resolution de novo structure prediction for small proteins publication-title: Science – volume: 29 start-page: 291 year: 2000 end-page: 325 ident: bib0046 article-title: Comparative protein structure modeling of genes and genomes publication-title: Annu. Rev. Biophys. Biomol. Struct. – volume: 58 start-page: 768 year: 2002 end-page: 776 ident: bib0032 article-title: Conformations of amino acids in proteins publication-title: Acta Crystallogr. Sect. D-Biol. Crystallogr. – volume: 59 start-page: 142 year: 2015 end-page: 157 ident: bib0006 article-title: APL: an angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction publication-title: Comput. Biol. Chem. – start-page: 1233 year: 2013 end-page: 1240 ident: bib0022 article-title: A knowledge-based genetic algorithm to predict three-dimensional structures of polypeptides publication-title: 2013 IEEE Congress on Evolutionary Computation (CEC) – start-page: 1285 year: 2016 end-page: 1292 ident: bib0058 article-title: Using crowding-distance in a multiobjective genetic algorithm for protein structure prediction publication-title: Proceedings.... Genetic and Evolutionary Computation Conference (GECCO 2016) – volume: 74 start-page: 1 year: 2009 end-page: 86 ident: bib0068 article-title: Common concepts for metaheuristics publication-title: Metaheuristics: from Design to Implementation – volume: 31 start-page: 3370 year: 2003 end-page: 3374 ident: bib0072 article-title: Lga: a method for finding 3d similarities in protein structures publication-title: Nucleic Acids Res. – volume: 22 start-page: 2577 year: 1983 end-page: 2637 ident: bib0035 article-title: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features publication-title: Biopolymers – volume: 32 start-page: W526 year: 2004 end-page: 531 ident: bib0037 article-title: Protein structure prediction and analysis using the Robetta server publication-title: Nucleic Acids Res. – volume: 12 start-page: 1350017 year: 2014 ident: bib0029 article-title: Is protein folding problem really a np-complete one? first investigations publication-title: J. Bioinf. Comput. Biol. – volume: 84 start-page: 51 year: 2016 end-page: 66 ident: bib0038 article-title: Evaluation of free modeling targets in CASP11 and ROLL publication-title: Proteins Struct. Funct. Bioinf. – year: 1989 ident: bib0049 article-title: On Evolution, Search, Optimization, Genetic Algorithms and Martial Arts: Towards Memetic Algorithms publication-title: Technical Report Caltech Concurrent Computation Program, Report. 826 – volume: 21 start-page: 319 year: 1995 end-page: 344 ident: bib0013 article-title: A novel approach to predicting protein structural classes in a (20–1)-d amino acid composition space publication-title: Proteins Struct. Funct. Bioinf. – volume: 82 start-page: 57 year: 2014 end-page: 83 ident: bib0067 article-title: Assessment of template-free modeling in CASP10 and ROLL publication-title: Proteins Struct. Funct. Bioinf. – volume: 26 start-page: 689 year: 2010 end-page: 691 ident: bib0011 article-title: Pyrosetta: a script-based interface for implementing molecular modeling algorithms using rosetta publication-title: Bioinformatics – volume: 6 start-page: 19 year: 1981 end-page: 30 ident: bib0063 article-title: Minimization by random search techniques publication-title: Math. Oper. Res. – volume: 268 start-page: 209 year: 1997 end-page: 225 ident: bib0062 article-title: Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions publication-title: J. Mol. Biol. – volume: 253 start-page: 164 year: 1991 end-page: 170 ident: bib0008 article-title: A method to identify protein sequences that fold into a known three-dimensional structure publication-title: Science – volume: 44 start-page: 547 year: 2003 end-page: 557 ident: bib0012 article-title: Ab initio methods publication-title: Structural Bioinformatics – volume: 11 start-page: 7 year: 2007 end-page: 21 ident: bib0003 article-title: Evolutionary computation and multimodal search: a good combination to tackle molecular diversity in the field of peptide design publication-title: Mol. Diversity – volume: 220 start-page: 671 year: 1983 end-page: 680 ident: bib0039 article-title: Optimization by simulated annealing publication-title: Science – volume: 13 start-page: S4 year: 2013 ident: bib0060 article-title: A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction publication-title: BMC Struct. Biol. – volume: 124 start-page: 83 year: 2012 end-page: 91 ident: bib0034 article-title: Bhageerath-targeting the near impossible: pushing the frontiers of atomic models for protein tertiary structure prediction publication-title: J. Chem. Sci. – volume: 76 start-page: 837 year: 2009 end-page: 851 ident: bib0061 article-title: Multiscale characterization of protein conformational ensembles publication-title: Proteins Struct. Funct. Bioinf. – volume: 1 start-page: 71 year: 2011 end-page: 88 ident: bib0017 article-title: Real-parameter evolutionary multimodal optimization-a survey of the state-of-the-art publication-title: Swarm Evol. Comput. – volume: 146 start-page: 141 year: 2010 end-page: 183 ident: bib0050 article-title: A modern introduction to memetic algorithms publication-title: Handbook of Metaheuristics – volume: 326 start-page: 1239 year: 2003 end-page: 1259 ident: bib0040 article-title: An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein–protein complexes publication-title: J. Mol. Biol. – volume: 237 start-page: 82 year: 2013 end-page: 117 ident: bib0007 article-title: A survey on optimization metaheuristics publication-title: Inf. Sci. – volume: 84 start-page: 4 year: 2016 end-page: 14 ident: bib0051 article-title: Critical assessment of methods of protein structure prediction: progress and new directions in round XI publication-title: Proteins Struct. Funct. Bioinf. – volume: 35 start-page: D61 year: 2007 end-page: D65 ident: bib0056 article-title: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins publication-title: Nucleic Acids Res. – volume: 4 start-page: 497 year: 2003 end-page: 502 ident: bib0016 article-title: The present view of the mechanism of protein folding publication-title: Nat. Rev. Mol. Cell. Biol. – volume: 9 start-page: 474 year: 2005 end-page: 488 ident: bib0041 article-title: A tutorial for competent memetic algorithms: model, taxonomy, and design issues publication-title: IEEE Trans. Evol. Comput. – volume: 526 start-page: 68 year: 2015 end-page: 74 ident: bib0014 article-title: A global reference for human genetic variation publication-title: Nature – start-page: 2 year: 1989 end-page: 9 ident: bib0066 article-title: Uniform Crossover in Genetic Algorithms publication-title: Proceedings of the 3rd International Conference on Genetic Algorithms. International Conference on Genetic Algorithms – year: 1976 ident: bib0018 article-title: The Selfish Gene – volume: 2 start-page: 187 year: 1993 end-page: 202 ident: bib0025 article-title: Real-coded genetic algorithms and interval-schemata publication-title: Foundations of Genetic Algorithms – volume: 39 start-page: 407 year: 1997 end-page: 460 ident: bib0053 article-title: Molecular modeling of proteins and mathematical prediction of protein structure publication-title: SIAM Rev. – volume: 57 start-page: 702 year: 2004 end-page: 710 ident: bib0074 article-title: Scoring function for automated assessment of protein structure template quality publication-title: Proteins Struct. Funct. Bioinf. – volume: 21 start-page: 167 year: 1995 end-page: 195 ident: bib0010 article-title: Funnels, pathways, and the energy landscape of protein folding: a synthesis publication-title: Proteins Struct. Funct. Bioinf. – volume: 49 start-page: 815 year: 2013 end-page: 820 ident: bib0027 article-title: A review of niching genetic algorithms for multimodal function optimization publication-title: Cybern. Syst. Anal. – volume: 18 start-page: 27 year: 2010 end-page: 63 ident: bib0047 article-title: Memetic algorithms for continuous optimisation based on local search chains publication-title: Evol. Comput. – volume: 23 start-page: 73 year: 1995 end-page: 82 ident: bib0024 article-title: Local moves: an efficient algorithm for simulation of protein folding publication-title: Proteins Struct. Funct. Bioinf. – volume: 10 start-page: 146 year: 2000 end-page: 152 ident: bib0055 article-title: Ab initio protein folding publication-title: Curr. Opin. Struct. Biol. – volume: 21 start-page: 1735 year: 2013 end-page: 1742 ident: bib0064 article-title: High-resolution comparative modeling with rosettacm publication-title: Structure – volume: PP year: 2016 ident: bib0015 article-title: A memetic algorithm for 3-d protein structure prediction problem publication-title: IEEE/ACM Trans. Comput. Biol. Bioinf. – volume: 32 start-page: W500 year: 2004 end-page: W502 ident: bib0031 article-title: Stride: a web server for secondary structure assignment from known atomic coordinates of proteins publication-title: Nucleic Acids Res. – volume: 6 start-page: 182 year: 2002 end-page: 197 ident: bib0019 article-title: A fast and elitist multiobjective genetic algorithm: NSGA-II publication-title: IEEE Trans. Evol. Comput. – volume: 181 start-page: 223 year: 1973 end-page: 230 ident: bib0001 article-title: Principles that govern the folding of protein chains publication-title: Science – volume: 383 start-page: 66 year: 2004 end-page: 93 ident: bib0059 article-title: Protein structure prediction using Rosetta publication-title: Methods Enzymol. – volume: 42 start-page: 623 year: 2008 end-page: 628 ident: bib0045 article-title: Radius of gyration as an indicator of protein structure compactness publication-title: J. Mol. Biol. – volume: 10 start-page: 139 year: 2000 end-page: 145 ident: bib0044 article-title: Effective energy functions for protein structure prediction publication-title: Curr. Opin. Struct. Biol. – volume: 24 start-page: 577 year: 2016 end-page: 607 ident: bib0026 article-title: Generating, maintaining and exploiting diversity in a memetic algorithm for protein structure prediction publication-title: Evol. Comput. – volume: 82 start-page: 164 year: 2014 end-page: 174 ident: bib0042 article-title: CASP10 results compared to those of previous CASP experiments publication-title: Proteins Struct. Funct. Bioinf. – volume: 2 start-page: 1382 year: 2004 end-page: 1389 ident: bib0070 article-title: Multimodal optimization using crowding-based differential evolution publication-title: 2004 IEEE Congress on Evolutionary Computation (CEC) – volume: 393 start-page: 249 year: 2009 end-page: 260 ident: bib0036 article-title: Sampling bottlenecks in de novo protein structure prediction publication-title: J. Mol. Biol. – volume: 84 start-page: 76 year: 2016 end-page: 86 ident: bib0073 article-title: Integration of quark and i-tasser for ab initio protein structure prediction in casp11 publication-title: Proteins Struct. Funct. Bioinf. – volume: 1 start-page: 25 year: 1993 end-page: 49 ident: bib0052 article-title: Predictive models for the breeder genetic algorithm i. Continuous parameter optimization publication-title: Evol. Comput. – volume: 28 start-page: 235 year: 2000 end-page: 242 ident: bib0004 article-title: The protein data bank publication-title: Nucleic Acids Res. – volume: 80 start-page: 1715 year: 2012 end-page: 1735 ident: bib0071 article-title: Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field publication-title: Proteins Struct. Funct. Bioinf. – volume: 8 start-page: 471 year: 1998 end-page: 475 ident: bib0020 article-title: Computer search algorithms in protein modification and design publication-title: Curr. Opin. Struct. Biol. – volume: 43 year: 2004 ident: bib0002 article-title: Bioinformatics: APractical Guide to the Analysis of Genes and Proteins – volume: 97 start-page: 10383 year: 2000 end-page: 10388 ident: bib0043 article-title: Native protein sequences are close to optimal for their structures publication-title: Proc. Natl. Acad. Sci. U.S.A. – start-page: 2709 year: 2011 end-page: 2716 ident: bib0021 article-title: A hybrid genetic algorithm for the 3-d protein structure prediction problem using a path-relinking strategy publication-title: 2011 IEEE Congress on Evolutionary Computation (CEC) – year: 2009 ident: bib0069 article-title: Benchmark functions for the CEC’2010 special session and competition on large-scale global optimization publication-title: Technical Report – start-page: 1 year: 2010 end-page: 8 ident: bib0048 article-title: MA-SW-Chains: Memetic algorithm based on local search chains for large scale continuous global optimization publication-title: 2010 IEEE Congress on Evolutionary Computation (CEC) – volume: 5 start-page: 24 year: 2010 ident: bib0054 article-title: Research frontier-memetic computation–past, present & future publication-title: IEEE Comput. Intell. Mag. – volume: 178 start-page: 63 year: 1984 end-page: 89 ident: bib0057 article-title: Solvent accessible surface area and excluded volume in proteins: analytical equations for overlapping spheres and implications for the hydrophobic effect publication-title: J. Mol. Biol. – volume: 4 start-page: 131 year: 1994 end-page: 140 ident: bib0028 article-title: Genetic algorithms and scatter search: unsuspected potentials publication-title: Stat. Comput. – start-page: 702 year: 2008 end-page: 711 ident: bib0030 article-title: Investigations into the effect of multiobjectivization in protein structure prediction publication-title: International Conference on Parallel Problem Solving from Nature – volume: 53 start-page: 251 year: 2014 end-page: 276 ident: bib0023 article-title: Three-dimensional protein structure prediction: methods and computational strategies publication-title: Comput. Biol. Chem. – volume: 24 start-page: 255 year: 2016 end-page: 265 ident: bib0005 article-title: Nias-server: neighbors influence of amino acids and secondary structures in proteins publication-title: J. Comput. Biol. – start-page: 1403 year: 2015 end-page: 1404 ident: bib0033 article-title: A memetic algorithm for protein structure prediction based on conformational preferences of aminoacid residues publication-title: Proceedings.... Genetic and Evolutionary Computation Conference (GECCO 2015) – volume: 6 start-page: 182 issue: 2 year: 2002 ident: 10.1016/j.cor.2017.11.015_bib0019 article-title: A fast and elitist multiobjective genetic algorithm: NSGA-II publication-title: IEEE Trans. Evol. Comput. doi: 10.1109/4235.996017 – volume: 11 start-page: 7 issue: 1 year: 2007 ident: 10.1016/j.cor.2017.11.015_bib0003 article-title: Evolutionary computation and multimodal search: a good combination to tackle molecular diversity in the field of peptide design publication-title: Mol. Diversity doi: 10.1007/s11030-006-9053-1 – year: 2009 ident: 10.1016/j.cor.2017.11.015_bib0069 article-title: Benchmark functions for the CEC’2010 special session and competition on large-scale global optimization – volume: 44 start-page: 547 year: 2003 ident: 10.1016/j.cor.2017.11.015_sbref0012 article-title: Ab initio methods – volume: 4 start-page: 131 issue: 2 year: 1994 ident: 10.1016/j.cor.2017.11.015_bib0028 article-title: Genetic algorithms and scatter search: unsuspected potentials publication-title: Stat. Comput. doi: 10.1007/BF00175357 – volume: 181 start-page: 223 issue: 4096 year: 1973 ident: 10.1016/j.cor.2017.11.015_bib0001 article-title: Principles that govern the folding of protein chains publication-title: Science doi: 10.1126/science.181.4096.223 – volume: 28 start-page: 235 issue: 1 year: 2000 ident: 10.1016/j.cor.2017.11.015_bib0004 article-title: The protein data bank publication-title: Nucleic Acids Res. doi: 10.1093/nar/28.1.235 – volume: 84 start-page: 76 issue: S1 year: 2016 ident: 10.1016/j.cor.2017.11.015_bib0073 article-title: Integration of quark and i-tasser for ab initio protein structure prediction in casp11 publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.24930 – volume: 35 start-page: D61 issue: suppl 1 year: 2007 ident: 10.1016/j.cor.2017.11.015_bib0056 article-title: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkl842 – volume: 24 start-page: 255 year: 2016 ident: 10.1016/j.cor.2017.11.015_bib0005 article-title: Nias-server: neighbors influence of amino acids and secondary structures in proteins publication-title: J. Comput. Biol. doi: 10.1089/cmb.2016.0074 – volume: 6 start-page: 19 issue: 1 year: 1981 ident: 10.1016/j.cor.2017.11.015_bib0063 article-title: Minimization by random search techniques publication-title: Math. Oper. Res. doi: 10.1287/moor.6.1.19 – year: 1976 ident: 10.1016/j.cor.2017.11.015_bib0018 – volume: 124 start-page: 83 issue: 1 year: 2012 ident: 10.1016/j.cor.2017.11.015_bib0034 article-title: Bhageerath-targeting the near impossible: pushing the frontiers of atomic models for protein tertiary structure prediction publication-title: J. Chem. Sci. doi: 10.1007/s12039-011-0189-x – year: 1989 ident: 10.1016/j.cor.2017.11.015_bib0049 article-title: On Evolution, Search, Optimization, Genetic Algorithms and Martial Arts: Towards Memetic Algorithms – start-page: 2709 year: 2011 ident: 10.1016/j.cor.2017.11.015_bib0021 article-title: A hybrid genetic algorithm for the 3-d protein structure prediction problem using a path-relinking strategy – volume: 26 start-page: 689 issue: 5 year: 2010 ident: 10.1016/j.cor.2017.11.015_bib0011 article-title: Pyrosetta: a script-based interface for implementing molecular modeling algorithms using rosetta publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq007 – volume: 526 start-page: 68 issue: 7571 year: 2015 ident: 10.1016/j.cor.2017.11.015_bib0014 article-title: A global reference for human genetic variation publication-title: Nature doi: 10.1038/nature15393 – volume: 309 start-page: 1868 issue: 5742 year: 2005 ident: 10.1016/j.cor.2017.11.015_bib0009 article-title: Toward high-resolution de novo structure prediction for small proteins publication-title: Science doi: 10.1126/science.1113801 – volume: 18 start-page: 27 issue: 1 year: 2010 ident: 10.1016/j.cor.2017.11.015_bib0047 article-title: Memetic algorithms for continuous optimisation based on local search chains publication-title: Evol. Comput. doi: 10.1162/evco.2010.18.1.18102 – volume: 22 start-page: 81 issue: 2 year: 1995 ident: 10.1016/j.cor.2017.11.015_bib0065 article-title: Linus: a hierarchic procedure to predict the fold of a protein publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.340220202 – volume: 8 start-page: 471 issue: 4 year: 1998 ident: 10.1016/j.cor.2017.11.015_bib0020 article-title: Computer search algorithms in protein modification and design publication-title: Curr. Opin. Struct. Biol. doi: 10.1016/S0959-440X(98)80125-5 – volume: 58 start-page: 768 issue: 5 year: 2002 ident: 10.1016/j.cor.2017.11.015_bib0032 article-title: Conformations of amino acids in proteins publication-title: Acta Crystallogr. Sect. D-Biol. Crystallogr. doi: 10.1107/S0907444902003359 – volume: 39 start-page: 407 issue: 3 year: 1997 ident: 10.1016/j.cor.2017.11.015_bib0053 article-title: Molecular modeling of proteins and mathematical prediction of protein structure publication-title: SIAM Rev. doi: 10.1137/S0036144594278060 – volume: 12 start-page: 1350017 issue: 01 year: 2014 ident: 10.1016/j.cor.2017.11.015_bib0029 article-title: Is protein folding problem really a np-complete one? first investigations publication-title: J. Bioinf. Comput. Biol. doi: 10.1142/S0219720013500170 – volume: 383 start-page: 66 year: 2004 ident: 10.1016/j.cor.2017.11.015_bib0059 article-title: Protein structure prediction using Rosetta publication-title: Methods Enzymol. doi: 10.1016/S0076-6879(04)83004-0 – volume: 74 start-page: 1 year: 2009 ident: 10.1016/j.cor.2017.11.015_sbref0068 article-title: Common concepts for metaheuristics – volume: 9 start-page: 474 issue: 5 year: 2005 ident: 10.1016/j.cor.2017.11.015_bib0041 article-title: A tutorial for competent memetic algorithms: model, taxonomy, and design issues publication-title: IEEE Trans. Evol. Comput. doi: 10.1109/TEVC.2005.850260 – volume: 76 start-page: 837 issue: 4 year: 2009 ident: 10.1016/j.cor.2017.11.015_bib0061 article-title: Multiscale characterization of protein conformational ensembles publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.22390 – start-page: 2 year: 1989 ident: 10.1016/j.cor.2017.11.015_bib0066 article-title: Uniform Crossover in Genetic Algorithms – volume: 59 start-page: 142 year: 2015 ident: 10.1016/j.cor.2017.11.015_bib0006 article-title: APL: an angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction publication-title: Comput. Biol. Chem. doi: 10.1016/j.compbiolchem.2015.08.006 – volume: 237 start-page: 82 year: 2013 ident: 10.1016/j.cor.2017.11.015_bib0007 article-title: A survey on optimization metaheuristics publication-title: Inf. Sci. doi: 10.1016/j.ins.2013.02.041 – volume: 5 start-page: 24 issue: 2 year: 2010 ident: 10.1016/j.cor.2017.11.015_bib0054 article-title: Research frontier-memetic computation–past, present & future publication-title: IEEE Comput. Intell. Mag. doi: 10.1109/MCI.2010.936309 – volume: 10 start-page: 146 issue: 2 year: 2000 ident: 10.1016/j.cor.2017.11.015_bib0055 article-title: Ab initio protein folding publication-title: Curr. Opin. Struct. Biol. doi: 10.1016/S0959-440X(00)00067-1 – volume: 21 start-page: 319 issue: 4 year: 1995 ident: 10.1016/j.cor.2017.11.015_bib0013 article-title: A novel approach to predicting protein structural classes in a (20–1)-d amino acid composition space publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.340210406 – volume: 80 start-page: 1715 issue: 7 year: 2012 ident: 10.1016/j.cor.2017.11.015_bib0071 article-title: Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.24065 – volume: PP issue: 99 year: 2016 ident: 10.1016/j.cor.2017.11.015_sbref0015 article-title: A memetic algorithm for 3-d protein structure prediction problem publication-title: IEEE/ACM Trans. Comput. Biol. Bioinf. – volume: 22 start-page: 2577 issue: 12 year: 1983 ident: 10.1016/j.cor.2017.11.015_bib0035 article-title: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features publication-title: Biopolymers doi: 10.1002/bip.360221211 – start-page: 1 year: 2010 ident: 10.1016/j.cor.2017.11.015_bib0048 article-title: MA-SW-Chains: Memetic algorithm based on local search chains for large scale continuous global optimization – volume: 57 start-page: 702 issue: 4 year: 2004 ident: 10.1016/j.cor.2017.11.015_bib0074 article-title: Scoring function for automated assessment of protein structure template quality publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.20264 – volume: 1 start-page: 71 issue: 2 year: 2011 ident: 10.1016/j.cor.2017.11.015_bib0017 article-title: Real-parameter evolutionary multimodal optimization-a survey of the state-of-the-art publication-title: Swarm Evol. Comput. doi: 10.1016/j.swevo.2011.05.005 – volume: 49 start-page: 815 issue: 6 year: 2013 ident: 10.1016/j.cor.2017.11.015_bib0027 article-title: A review of niching genetic algorithms for multimodal function optimization publication-title: Cybern. Syst. Anal. doi: 10.1007/s10559-013-9570-8 – start-page: 1285 year: 2016 ident: 10.1016/j.cor.2017.11.015_bib0058 article-title: Using crowding-distance in a multiobjective genetic algorithm for protein structure prediction – volume: 84 start-page: 4 issue: S1 year: 2016 ident: 10.1016/j.cor.2017.11.015_bib0051 article-title: Critical assessment of methods of protein structure prediction: progress and new directions in round XI publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.25064 – volume: 84 start-page: 51 issue: S1 year: 2016 ident: 10.1016/j.cor.2017.11.015_bib0038 article-title: Evaluation of free modeling targets in CASP11 and ROLL publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.24973 – volume: 4 start-page: 497 issue: 6 year: 2003 ident: 10.1016/j.cor.2017.11.015_bib0016 article-title: The present view of the mechanism of protein folding publication-title: Nat. Rev. Mol. Cell. Biol. doi: 10.1038/nrm1126 – start-page: 1233 year: 2013 ident: 10.1016/j.cor.2017.11.015_bib0022 article-title: A knowledge-based genetic algorithm to predict three-dimensional structures of polypeptides – volume: 53 start-page: 251 year: 2014 ident: 10.1016/j.cor.2017.11.015_bib0023 article-title: Three-dimensional protein structure prediction: methods and computational strategies publication-title: Comput. Biol. Chem. doi: 10.1016/j.compbiolchem.2014.10.001 – volume: 82 start-page: 57 issue: S2 year: 2014 ident: 10.1016/j.cor.2017.11.015_bib0067 article-title: Assessment of template-free modeling in CASP10 and ROLL publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.24470 – volume: 31 start-page: 3370 issue: 13 year: 2003 ident: 10.1016/j.cor.2017.11.015_bib0072 article-title: Lga: a method for finding 3d similarities in protein structures publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkg571 – volume: 32 start-page: W500 issue: suppl 2 year: 2004 ident: 10.1016/j.cor.2017.11.015_bib0031 article-title: Stride: a web server for secondary structure assignment from known atomic coordinates of proteins publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkh429 – volume: 178 start-page: 63 issue: 1 year: 1984 ident: 10.1016/j.cor.2017.11.015_bib0057 article-title: Solvent accessible surface area and excluded volume in proteins: analytical equations for overlapping spheres and implications for the hydrophobic effect publication-title: J. Mol. Biol. doi: 10.1016/0022-2836(84)90231-6 – start-page: 702 year: 2008 ident: 10.1016/j.cor.2017.11.015_bib0030 article-title: Investigations into the effect of multiobjectivization in protein structure prediction – volume: 2 start-page: 187 year: 1993 ident: 10.1016/j.cor.2017.11.015_bib0025 article-title: Real-coded genetic algorithms and interval-schemata – volume: 10 start-page: 139 issue: 2 year: 2000 ident: 10.1016/j.cor.2017.11.015_bib0044 article-title: Effective energy functions for protein structure prediction publication-title: Curr. Opin. Struct. Biol. doi: 10.1016/S0959-440X(00)00063-4 – volume: 393 start-page: 249 issue: 1 year: 2009 ident: 10.1016/j.cor.2017.11.015_bib0036 article-title: Sampling bottlenecks in de novo protein structure prediction publication-title: J. Mol. Biol. doi: 10.1016/j.jmb.2009.07.063 – volume: 29 start-page: 291 issue: 1 year: 2000 ident: 10.1016/j.cor.2017.11.015_bib0046 article-title: Comparative protein structure modeling of genes and genomes publication-title: Annu. Rev. Biophys. Biomol. Struct. doi: 10.1146/annurev.biophys.29.1.291 – volume: 24 start-page: 577 issue: 4 year: 2016 ident: 10.1016/j.cor.2017.11.015_bib0026 article-title: Generating, maintaining and exploiting diversity in a memetic algorithm for protein structure prediction publication-title: Evol. Comput. doi: 10.1162/EVCO_a_00176 – volume: 43 year: 2004 ident: 10.1016/j.cor.2017.11.015_bib0002 – start-page: 1403 year: 2015 ident: 10.1016/j.cor.2017.11.015_bib0033 article-title: A memetic algorithm for protein structure prediction based on conformational preferences of aminoacid residues – volume: 21 start-page: 167 issue: 3 year: 1995 ident: 10.1016/j.cor.2017.11.015_bib0010 article-title: Funnels, pathways, and the energy landscape of protein folding: a synthesis publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.340210302 – volume: 253 start-page: 164 issue: 5016 year: 1991 ident: 10.1016/j.cor.2017.11.015_bib0008 article-title: A method to identify protein sequences that fold into a known three-dimensional structure publication-title: Science doi: 10.1126/science.1853201 – volume: 220 start-page: 671 issue: 4598 year: 1983 ident: 10.1016/j.cor.2017.11.015_bib0039 article-title: Optimization by simulated annealing publication-title: Science doi: 10.1126/science.220.4598.671 – volume: 13 start-page: S4 issue: Suppl 1 year: 2013 ident: 10.1016/j.cor.2017.11.015_bib0060 article-title: A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction publication-title: BMC Struct. Biol. doi: 10.1186/1472-6807-13-S1-S4 – volume: 21 start-page: 1735 issue: 10 year: 2013 ident: 10.1016/j.cor.2017.11.015_bib0064 article-title: High-resolution comparative modeling with rosettacm publication-title: Structure doi: 10.1016/j.str.2013.08.005 – volume: 82 start-page: 164 issue: S2 year: 2014 ident: 10.1016/j.cor.2017.11.015_bib0042 article-title: CASP10 results compared to those of previous CASP experiments publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.24448 – volume: 2 start-page: 1382 year: 2004 ident: 10.1016/j.cor.2017.11.015_bib0070 article-title: Multimodal optimization using crowding-based differential evolution – volume: 97 start-page: 10383 issue: 19 year: 2000 ident: 10.1016/j.cor.2017.11.015_bib0043 article-title: Native protein sequences are close to optimal for their structures publication-title: Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.97.19.10383 – volume: 146 start-page: 141 year: 2010 ident: 10.1016/j.cor.2017.11.015_bib0050 article-title: A modern introduction to memetic algorithms – volume: 23 start-page: 73 issue: 1 year: 1995 ident: 10.1016/j.cor.2017.11.015_bib0024 article-title: Local moves: an efficient algorithm for simulation of protein folding publication-title: Proteins Struct. Funct. Bioinf. doi: 10.1002/prot.340230109 – volume: 326 start-page: 1239 issue: 4 year: 2003 ident: 10.1016/j.cor.2017.11.015_bib0040 article-title: An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein–protein complexes publication-title: J. Mol. Biol. doi: 10.1016/S0022-2836(03)00021-4 – volume: 42 start-page: 623 issue: 4 year: 2008 ident: 10.1016/j.cor.2017.11.015_bib0045 article-title: Radius of gyration as an indicator of protein structure compactness publication-title: J. Mol. Biol. doi: 10.1134/S0026893308040195 – volume: 1 start-page: 25 issue: 1 year: 1993 ident: 10.1016/j.cor.2017.11.015_bib0052 article-title: Predictive models for the breeder genetic algorithm i. Continuous parameter optimization publication-title: Evol. Comput. doi: 10.1162/evco.1993.1.1.25 – volume: 32 start-page: W526 year: 2004 ident: 10.1016/j.cor.2017.11.015_sbref0037 article-title: Protein structure prediction and analysis using the Robetta server publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkh468 – volume: 268 start-page: 209 issue: 1 year: 1997 ident: 10.1016/j.cor.2017.11.015_bib0062 article-title: Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions publication-title: J. Mol. Biol. doi: 10.1006/jmbi.1997.0959 |
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| Snippet | •An algorithm to deal with the 3-D protein structure prediction problem is proposed.•The method is a multimodal evolutionary algorithm allied to a local search... Tertiary protein structure prediction is a challenging problem in Structural Bioinformatics and is classified according to the computational complexity theory... |
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| SubjectTerms | Algorithms Bioinformatics Complexity theory Data banks Evolutionary algorithms Hybrid evolutionary algorithms Metaheuristics Multimodal optimization Operations research Operators Predictions Proteins PSP problem Searching Structural Bioinformatics Studies Three dimensional analysis |
| Title | Three-dimensional protein structure prediction based on memetic algorithms |
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