메뉴 건너뛰기




Volumn 17, Issue 4, 2013, Pages 558-576

Clustered memetic algorithm with local heuristics for ab initio protein structure prediction

Author keywords

Clustered memetic algorithm; Meme incorporation; Pull move; Reverse pull move; Self avoiding walk (SAW)

Indexed keywords

BASINS OF ATTRACTION; DOMAIN-SPECIFIC KNOWLEDGE; MEME INCORPORATION; MEMETIC ALGORITHMS; PROTEIN STRUCTURE PREDICTION; PULL MOVES; SELF AVOIDING WALK; STRUCTURE PREDICTION;

EID: 84881171144     PISSN: 1089778X     EISSN: None     Source Type: Journal    
DOI: 10.1109/TEVC.2012.2213258     Document Type: Article
Times cited : (37)

References (62)
  • 1
    • 21644447473 scopus 로고    scopus 로고
    • Editorial: So much more to know
    • D. Kennedy and C. Norman, "Editorial: So much more to know," Science, vol. 309, no. 5731, pp. 78-102, 2005.
    • (2005) Science , vol.309 , Issue.5731 , pp. 78-102
    • Kennedy, D.1    Norman, C.2
  • 3
    • 0031897962 scopus 로고    scopus 로고
    • Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete
    • B. Berger and T. Leighton, "Protein folding in the hydrophobichydrophilic (HP) model is NP-complete," J. Computat. Biol., vol. 5, no. 1, pp. 27-40, 1998. (Pubitemid 28153003)
    • (1998) Journal of Computational Biology , vol.5 , Issue.1 , pp. 27-40
    • Berger, B.1    Leighton, T.2
  • 4
    • 0030015087 scopus 로고    scopus 로고
    • Fast protein folding in the hydrophobichydrophilic model within three-eighths of optimal
    • W. E. Hart and S. C. Istrail, "Fast protein folding in the hydrophobichydrophilic model within three-eighths of optimal," J. Computat. Biol., vol. 3, no. 1, pp. 53-96, 1996.
    • (1996) J. Computat. Biol , vol.3 , Issue.1 , pp. 53-96
    • Hart, W.E.1    Istrail, S.C.2
  • 6
    • 0033117917 scopus 로고    scopus 로고
    • New Monte Carlo algorithms for protein folding
    • DOI 10.1016/S0959-440X(99)80025-6
    • U. H. Hansmann and Y. Okamoto, "New Monte Carlo algorithms for protein folding," Current Opinion Structural Biol., vol. 9, no. 1, pp. 177-183, 1999. (Pubitemid 29452895)
    • (1999) Current Opinion in Structural Biology , vol.9 , Issue.2 , pp. 177-183
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 7
    • 36048965924 scopus 로고    scopus 로고
    • A replica exchange Monte Carlo algorithm for protein folding in the HP model
    • C. Thachuk, A. Shmygelska, and H. H. Hoosr, "A replica exchange Monte Carlo algorithm for protein folding in the HP model," BMC Bioinformatics, vol. 8, no. 342, 2007.
    • (2007) BMC Bioinformatics , vol.8 , pp. 342
    • Thachuk, C.1    Shmygelska, A.2    Hoosr, H.H.3
  • 8
    • 4344594052 scopus 로고    scopus 로고
    • An immune algorithm with hyper-macromutations for the Dill's 2-D hydrophobic-hydrophilic model
    • Jun
    • V. Cutello, G. Nicosia, and M. Pavone, "An immune algorithm with hyper-macromutations for the Dill's 2-D hydrophobic-hydrophilic model," in Proc. IEEE CEC, Jun. 2004, pp. 1074-1080.
    • (2004) Proc. IEEE CEC , pp. 1074-1080
    • Cutello, V.1    Nicosia, G.2    Pavone, M.3
  • 10
    • 33947230224 scopus 로고    scopus 로고
    • An immune algorithm for protein structure prediction on lattice models
    • DOI 10.1109/TEVC.2006.880328
    • V. Cutello, G. Nicosia, M. Pavone, and J. Timmis, "An immune algorithm for protein structure prediction on lattice models," IEEE Trans. Evol. Comput., vol. 11, no. 1, pp. 101-117, Feb. 2007. (Pubitemid 46421671)
    • (2007) IEEE Transactions on Evolutionary Computation , vol.11 , Issue.1 , pp. 101-117
    • Cutello, V.1    Nicosia, G.2    Pavone, M.3    Timmis, J.4
  • 11
    • 0027245418 scopus 로고
    • Genetic algorithms for protein folding simulations
    • DOI 10.1006/jmbi.1993.1258
    • R. Unger and J. Moult, "Genetic algorithms for protein folding simulations," J. Molecular Biol., vol. 231, no. 1, pp. 75-81, 1993. (Pubitemid 23186599)
    • (1993) Journal of Molecular Biology , vol.231 , Issue.1 , pp. 75-81
    • Unger, R.1    Moult, J.2
  • 13
    • 0005864682 scopus 로고    scopus 로고
    • Protein structure prediction as a hard optimization problem: The genetic algorithm approach
    • M. M. Khimasia and P. V. Coveney, "Protein structure prediction as a hard optimization problem: The genetic algorithm approach," Molecular Simulation, vol. 19, no. 4, pp. 205-226, 1997. (Pubitemid 127499759)
    • (1997) Molecular Simulation , vol.19 , Issue.4 , pp. 205-226
    • Khimasia, M.M.1    Coveney, P.V.2
  • 17
    • 56649124808 scopus 로고    scopus 로고
    • Protein folding prediction in 3-D FCC HP lattice model using genetic algorithm
    • M. Hoque, M. Chetty, and A. Sattar, "Protein folding prediction in 3-D FCC HP lattice model using genetic algorithm," in Proc. IEEE CEC, Sep. 2007, pp. 4138-4145.
    • (2007) Proc. IEEE CEC, Sep , pp. 4138-4145
    • Hoque, M.1    Chetty, M.2    Sattar, A.3
  • 19
    • 25444462754 scopus 로고    scopus 로고
    • An ant colony optimization algorithm for the 2-D and 3-D hydrophobic polar protein folding problem
    • A. Shmygelska and H. H. Hoos, "An ant colony optimization algorithm for the 2-D and 3-D hydrophobic polar protein folding problem," BMC Bioinformatics, vol. 6, no. 30, 2005.
    • (2005) BMC Bioinformatics , vol.6 , pp. 30
    • Shmygelska, A.1    Hoos, H.H.2
  • 21
    • 84877955201 scopus 로고    scopus 로고
    • Protein folding in the HPmodel solved with a hybrid population based ACO algorithm
    • T. Thalheim, D. Merkle, and M. Middendorf, "Protein folding in the HPmodel solved with a hybrid population based ACO algorithm," IAENG Int. J. Comput. Sci., vol. 35, no. 3, pp. 291-300, 2008.
    • (2008) IAENG Int. J. Comput. Sci , vol.35 , Issue.3 , pp. 291-300
    • Thalheim, T.1    Merkle, D.2    Middendorf, M.3
  • 23
    • 49049097947 scopus 로고    scopus 로고
    • Protein folding in simplified models with estimation of distribution algorithms
    • Aug
    • R. Santana, P. Larraaga, and J. A. Lozano, "Protein folding in simplified models with estimation of distribution algorithms," IEEE Trans. Evol. Comput., vol. 12, no. 4, pp. 418-438, Aug. 2008.
    • (2008) IEEE Trans. Evol. Comput , vol.12 , Issue.4 , pp. 418-438
    • Santana, R.1    Larraaga, P.2    Lozano, J.A.3
  • 24
    • 0002006297 scopus 로고
    • Are there pathaways for protein folding?
    • C. Levinthal, "Are there pathaways for protein folding?" J. Chim. Phys. Phys. Chim. Biol., vol. 65, pp. 44-45, 1968.
    • (1968) J. Chim. Phys. Phys. Chim. Biol , vol.65 , pp. 44-45
    • Levinthal, C.1
  • 25
    • 34347375915 scopus 로고    scopus 로고
    • The protein folding problem: When will it be solved?
    • DOI 10.1016/j.sbi.2007.06.001, PII S0959440X07000772, Nucleic acids / Sequences and topology
    • K. A. Dill, S. B. Ozkan, T. R. Weikl, J. D. Chodera, and V. A. Voelz, "The protein folding problem: When will it be solved," Current Opinion Structural Biol., vol. 17, no. 3, pp. 342-346, 2007. (Pubitemid 47021366)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.3 , pp. 342-346
    • Dill, K.A.1    Ozkan, S.B.2    Weikl, T.R.3    Chodera, J.D.4    Voelz, V.A.5
  • 26
    • 34748820002 scopus 로고    scopus 로고
    • A memetic algorithm and a tabu search for the multi-compartment vehicle routing problem
    • DOI 10.1016/j.cor.2006.10.006, PII S0305054806002516, Algorithms and Computational Methods in Feasibility and Infeasibility
    • A. Fallahi, C. Prins, and R. W. Calvo, "A memetic algorithm and a tabu search for the multicompartment vehicle routing problem," Comput. Oper. Res., vol. 35, no. 5, pp. 1725-1741, 2008. (Pubitemid 47488641)
    • (2008) Computers and Operations Research , vol.35 , Issue.5 , pp. 1725-1741
    • Fallahi, A.1    Prins, C.2    Wolfler Calvo, R.3
  • 30
    • 35048823896 scopus 로고    scopus 로고
    • A memetic algorithm for protein structure prediction in a 3-D lattice HP model
    • Berlin/Heidelberg, Germany: Springer
    • A. Bazzoli and A. G. Tettamanzi, "A memetic algorithm for protein structure prediction in a 3-D lattice HP model," in Applications of Evolutionary Computing (Lecture Notes in Computer Science, vol. 3005). Berlin/Heidelberg, Germany: Springer, 2004, pp. 1-10.
    • (2004) Applications of Evolutionary Computing (Lecture Notes in Computer Science , vol.3005 , pp. 1-10
    • Bazzoli, A.1    Tettamanzi, A.G.2
  • 31
    • 33847680283 scopus 로고    scopus 로고
    • Multimeme algorithms using fuzzy logic based MEMES for protein structure prediction
    • W. Hart, J. Smith, and N. Krasnogor, Eds. Berlin/Heidelberg, Germany: Springer
    • D. Pelta and N. Krasnogor, "Multimeme algorithms using fuzzy logic based MEMES for protein structure prediction," in Recent Advances in Memetic Algorithms (Studies in Fuzziness and Soft Computing, vol. 166), W. Hart, J. Smith, and N. Krasnogor, Eds. Berlin/Heidelberg, Germany: Springer, 2005, pp. 49-64.
    • (2005) Recent Advances in Memetic Algorithms (Studies in Fuzziness and Soft Computing , vol.166 , pp. 49-64
    • Pelta, D.1    Krasnogor, N.2
  • 32
    • 27344436852 scopus 로고    scopus 로고
    • The co-evolution of memetic algorithms for protein structure prediction
    • W. Hart, J. Smith, and N. Krasnogor, Eds. Berlin/Heidelberg, Germany: Springer
    • J. Smith, "The co-evolution of memetic algorithms for protein structure prediction," in Recent Advances in Memetic Algorithms (Studies in Fuzziness and Soft Computing, vol. 166), W. Hart, J. Smith, and N. Krasnogor, Eds. Berlin/Heidelberg, Germany: Springer, 2005, pp. 105-128.
    • (2005) Recent Advances in Memetic Algorithms (Studies in Fuzziness and Soft Computing , vol.166 , pp. 105-128
    • Smith, J.1
  • 34
    • 0024750637 scopus 로고
    • A lattice statistical mechanics model of the conformational and sequence spaces of proteins
    • K. F. Lau and K. A. Dill, "A lattice statistical mechanics model of the conformational and sequence spaces of proteins," Macromolecules, vol. 22, no. 10, pp. 3986-3997, 1989.
    • (1989) Macromolecules , vol.22 , Issue.10 , pp. 3986-3997
    • Lau, K.F.1    Dill, K.A.2
  • 35
    • 0032606133 scopus 로고    scopus 로고
    • Ab initio protein structure prediction using a combined hierarchical approach
    • DOI 10.1002/(SICI)1097-0134(1999)37:3+<194::AID-PROT24>3.0.CO;2-F
    • R. Samudrala, Y. Xia, and E. Huang, "Ab initio protein structure prediction using a combined hierarchical approach," Proteins Structure Function Bioinformatics, vol. 37, no. 3, pp. 194-198, 1999. (Pubitemid 29463531)
    • (1999) Proteins: Structure, Function and Genetics , vol.37 , Issue.SUPPL. 3 , pp. 194-198
    • Samudrala, R.1    Xia, Y.2    Huang, E.3    Levitt, M.4
  • 36
    • 0034733381 scopus 로고    scopus 로고
    • Ab initio construction of protein tertiary structures using a hierarchical approach
    • Y. Xia, E. S. Huang, M. Levitt, and R. Samudrala, "Ab initio construction of protein tertiary structures using a hierarchical approach," J. Molecular Biol., vol. 300, no. 1, pp. 171-185, 2000.
    • (2000) J. Molecular Biol , vol.300 , Issue.1 , pp. 171-185
    • Xia, Y.1    Huang, E.S.2    Levitt, M.3    Samudrala, R.4
  • 39
    • 0034031680 scopus 로고    scopus 로고
    • Effective energy functions for protein structure prediction
    • DOI 10.1016/S0959-440X(00)00063-4
    • T. Lazaridis and M. Karplus, "Effective energy function for proteins in solution," Current Opinion Structural Biol., vol. 10, no. 2, pp. 139-145, 2000. (Pubitemid 30198938)
    • (2000) Current Opinion in Structural Biology , vol.10 , Issue.2 , pp. 139-145
    • Lazaridis, T.1    Karplus, M.2
  • 42
    • 50249137639 scopus 로고    scopus 로고
    • Nonisomorphic coding in lattice model and its impact for protein folding prediction using genetic algorithm
    • T. Hoque, M. Chetty, and L. S. Dooley, "Nonisomorphic coding in lattice model and its impact for protein folding prediction using genetic algorithm," in Proc. IEEE Symp. Comput. Intell. Bioinformatics Comput. Biol., 2006, pp. 28-29.
    • (2006) Proc. IEEE Symp. Comput. Intell. Bioinformatics Comput. Biol , pp. 28-29
    • Hoque, T.1    Chetty, M.2    Dooley, L.S.3
  • 43
    • 79959487834 scopus 로고    scopus 로고
    • An unorthodox introduction to memetic algorithms
    • N. Krasnogor, "An unorthodox introduction to memetic algorithms," ACM SIGEVOlution, vol. 3, no. 4, pp. 6-15, 2008.
    • (2008) ACM SIGEVOlution , vol.3 , Issue.4 , pp. 6-15
    • Krasnogor, N.1
  • 45
    • 0009597802 scopus 로고
    • Memes: The new replicators
    • Oxford, U.K.: Oxford Univ. Press, ch. 11
    • R. Dawkins, "Memes: The new replicators," in The Selfish Gene. Oxford, U.K.: Oxford Univ. Press, 1976, ch. 11, pp. 203-215.
    • (1976) The Selfish Gene , pp. 203-215
    • Dawkins, R.1
  • 50
    • 79959431132 scopus 로고    scopus 로고
    • Clustered memetic algorithm for protein structure prediction
    • Jul
    • M. K. Islam and M. Chetty, "Clustered memetic algorithm for protein structure prediction," in Proc. IEEE CEC, Jul. 2010.
    • (2010) Proc. IEEE CEC
    • Islam, M.K.1    Chetty, M.2
  • 51
    • 44949145113 scopus 로고    scopus 로고
    • Progress and challenges in protein structure prediction
    • Y. Zhang, "Progress and challenges in protein structure prediction," Current Opinion Structural Biol., vol. 18, no. 3, pp. 342-348, 2008.
    • (2008) Current Opinion Structural Biol , vol.18 , Issue.3 , pp. 342-348
    • Zhang, Y.1
  • 55
    • 0031082540 scopus 로고    scopus 로고
    • Multimodal function optimization using minimal representation size clustering and its application to planning multipaths
    • C. Hocaoǧglu and A. C. Sanderson, "Multimodal function optimization using minimal representation size clustering and its application to planning multipaths," Evol. Comput., vol. 5, no. 1, pp. 81-104, 1997. (Pubitemid 127717839)
    • (1997) Evolutionary Computation , vol.5 , Issue.1 , pp. 81-104
    • Hocaoglu, C.1    Sanderson, A.C.2
  • 60
    • 0037258333 scopus 로고    scopus 로고
    • Growth algorithms for lattice heteropolymers at low temperatures
    • H.-P. Hsu, V. Mehra, W. Nadler, and P. Grassberger, "Growth algorithms for lattice heteropolymers at low temperatures," J. Chem. Phys., vol. 118, no. 1, pp. 444-451, 2003.
    • (2003) J. Chem. Phys , vol.118 , Issue.1 , pp. 444-451
    • Hsu, H.-P.1    Mehra, V.2    Nadler, W.3    Grassberger, P.4
  • 61
    • 0142045029 scopus 로고    scopus 로고
    • Improving genetic algorithms for protein folding simulations by systematic crossover
    • DOI 10.1016/S0303-2647(98)00090-2, PII S0303264798000902
    • R. König and T. Dandekar, "Improving genetic algorithms for protein folding simulations by systematic crossover," Biosystems, vol. 50, no. 1, pp. 17-25, Apr. 1999. (Pubitemid 29099757)
    • (1999) BioSystems , vol.50 , Issue.1 , pp. 17-25
    • Konig, R.1    Dandekar, T.2
  • 62
    • 35248858298 scopus 로고    scopus 로고
    • Protein structure prediction using evolutionary algorithms hybridized with backtracking
    • J. Mira and J. lvarez, Eds. Berlin/Heidelberg, Germany: Springer
    • C. Cotta, "Protein structure prediction using evolutionary algorithms hybridized with backtracking," in Artificial Neural Nets Problem Solving Methods (Lecture Notes in Computer Science, vol. 2687), J. Mira and J. lvarez, Eds. Berlin/Heidelberg, Germany: Springer, 2003, pp. 1044-1044.
    • (2003) Artificial Neural Nets Problem Solving Methods (Lecture Notes in Computer Science , vol.2687 , pp. 1044-1044
    • Cotta, C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.