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Volumn 27, Issue , 2014, Pages 70-79

Protein secondary structure optimization using an improved artificial bee colony algorithm based on AB off-lattice model

Author keywords

AB off lattice model; Artificial Bee Colony algorithm (ABC); Convergence of algorithm; Protein secondary structure optimization

Indexed keywords

AB OFF-LATTICE MODELS; ARTIFICIAL BEE COLONY ALGORITHMS; ARTIFICIAL BEE COLONY ALGORITHMS (ABC); CONVERGENCE PERFORMANCE; PREDICTING THE SECONDARY STRUCTURES; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE PREDICTION; SWARM INTELLIGENCE ALGORITHMS;

EID: 84888306730     PISSN: 09521976     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.engappai.2013.06.010     Document Type: Article
Times cited : (76)

References (38)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • C.B. Anfinsen Principles that govern the folding of protein chains Science 181 96 1973 223 230
    • (1973) Science , vol.181 , Issue.96 , pp. 223-230
    • Anfinsen, C.B.1
  • 2
    • 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 hydrophobic-hydrophilic (HP) model is NP-complete J. Comput. Biol. 5 1 1998 27 40
    • (1998) J. Comput. Biol. , vol.5 , Issue.1 , pp. 27-40
    • Berger, B.1    Leighton, T.2
  • 3
    • 19644381706 scopus 로고    scopus 로고
    • High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein
    • T.K Chiu, J. Kubelka, R. Herbst-Irmer, W.A. Eaton, J. Hofrichter, and D.R. Davies High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein Proc. Natl. Acad. Sci. USA 102 21 2005 7517 7522
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , Issue.21 , pp. 7517-7522
    • Chiu, T.K.1    Kubelka, J.2    Herbst-Irmer, R.3    Eaton, W.A.4    Hofrichter, J.5    Davies, D.R.6
  • 4
    • 47149117454 scopus 로고    scopus 로고
    • Evolution of genes and genomes on the Drosophila phylogeny
    • A.G. Clark Evolution of genes and genomes on the Drosophila phylogeny Nature 450 7167 2007 203 218
    • (2007) Nature , vol.450 , Issue.7167 , pp. 203-218
    • Clark, A.G.1
  • 5
    • 48449106792 scopus 로고    scopus 로고
    • The Jpred 3 secondary structure prediction server
    • C. Cole, J.D. Barber, and G.J. Barton The Jpred 3 secondary structure prediction server Nucleic Acids Res. 36 2008 W197 W201
    • (2008) Nucleic Acids Res. , vol.36
    • Cole, C.1    Barber, J.D.2    Barton, G.J.3
  • 6
    • 33947230224 scopus 로고    scopus 로고
    • An immune algorithm for protein structure prediction on lattice models
    • V. Cutello, G. Nicosia, M. Pavone, and J. Timmis An immune algorithm for protein structure prediction on lattice models IEEE Trans. Evol. Comput. 11 1 2007 101 117
    • (2007) IEEE Trans. Evol. Comput. , vol.11 , Issue.1 , pp. 101-117
    • Cutello, V.1    Nicosia, G.2    Pavone, M.3    Timmis, J.4
  • 7
    • 79959282672 scopus 로고    scopus 로고
    • Improved artificial bee colony algorithm for global optimization
    • W. Gao, and S. Liu Improved artificial bee colony algorithm for global optimization Inform. Process. Lett. 111 17 2011 871 882
    • (2011) Inform. Process. Lett. , vol.111 , Issue.17 , pp. 871-882
    • Gao, W.1    Liu, S.2
  • 8
    • 2442482810 scopus 로고    scopus 로고
    • Autophagy as a cell death and tumor suppressor mechanism
    • D. Gozuacik, and K. Adi Autophagy as a cell death and tumor suppressor mechanism Oncogene 16 16 2004 2891 2906
    • (2004) Oncogene , vol.16 , Issue.16 , pp. 2891-2906
    • Gozuacik, D.1    Adi, K.2
  • 10
    • 84988761672 scopus 로고    scopus 로고
    • Structure optimization in an off-lattice protein model
    • H-P Hsu, V. Mehra, and P. Grassberger Structure optimization in an off-lattice protein model Phys. Rev. E 68 3 2003 037703
    • (2003) Phys. Rev. e , vol.68 , Issue.3 , pp. 037703
    • Hsu, H.-P.1    Mehra, V.2    Grassberger, P.3
  • 11
    • 14744280111 scopus 로고    scopus 로고
    • Prediction of the secondary structure of proteins using PREDICT, a nearest neighbor method on pattern space
    • K. Joo, I. Kim, S.Y. Kim, J. Lee, J. Lee, and S.J. Lee Prediction of the secondary structure of proteins using PREDICT, a nearest neighbor method on pattern space J. Kor. Phys. Soc. 45 2004 1441 1449
    • (2004) J. Kor. Phys. Soc. , vol.45 , pp. 1441-1449
    • Joo, K.1    Kim, I.2    Kim, S.Y.3    Lee, J.4    Lee, J.5    Lee, S.J.6
  • 12
    • 84873671929 scopus 로고    scopus 로고
    • Artificial bee colony algorithm and pattern search hybridized for global optimization
    • F. Kang, J. Li, and H. Li Artificial bee colony algorithm and pattern search hybridized for global optimization Appl. Soft Comput. 13 4 2013 1781 1791
    • (2013) Appl. Soft Comput. , vol.13 , Issue.4 , pp. 1781-1791
    • Kang, F.1    Li, J.2    Li, H.3
  • 13
    • 35148827874 scopus 로고    scopus 로고
    • An idea based on honey bee swarm for numerical optimization
    • Erciyes University, Engineering Faculty, Computer Engineering Department
    • Karaboga, D., 2005. An Idea Based on Honey Bee Swarm for Numerical Optimization. Technical Report-TR06. Erciyes University, Engineering Faculty, Computer Engineering Department.
    • (2005) Technical Report-TR06
    • Karaboga, D.1
  • 15
    • 27244454789 scopus 로고    scopus 로고
    • Structure optimization by conformational space annealing in an off-lattice protein model
    • S-Y. Kim, S.B. Lee, and J. Lee Structure optimization by conformational space annealing in an off-lattice protein model Phys. Rev. E 72 1 2005 011916
    • (2005) Phys. Rev. e , vol.72 , Issue.1 , pp. 011916
    • Kim, S.-Y.1    Lee, S.B.2    Lee, J.3
  • 18
    • 84874405259 scopus 로고    scopus 로고
    • Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment
    • Y. Li, H. Liu, I. Rata, and E. Jakobsson Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment J. Chem. Inform. Model. 53 2 2013 500 508
    • (2013) J. Chem. Inform. Model. , vol.53 , Issue.2 , pp. 500-508
    • Li, Y.1    Liu, H.2    Rata, I.3    Jakobsson, E.4
  • 21
    • 58649083223 scopus 로고    scopus 로고
    • Protein secondary structure prediction using three neural networks and a segmental semi Markov model
    • S.A. Malekpour, S. Naghizadeh, and H. Pezeshk Protein secondary structure prediction using three neural networks and a segmental semi Markov model Math. Biosci. 217 2 2009 145 150
    • (2009) Math. Biosci. , vol.217 , Issue.2 , pp. 145-150
    • Malekpour, S.A.1    Naghizadeh, S.2    Pezeshk, H.3
  • 22
    • 84870062063 scopus 로고    scopus 로고
    • Design of frequency response masking FIR filter in the Canonic Signed Digit space using modified Artificial Bee Colony algorithm
    • M. Manuel, and E. Elias Design of frequency response masking FIR filter in the Canonic Signed Digit space using modified Artificial Bee Colony algorithm Eng. Appl. Artif. Intell. 26 1 2013 660 668
    • (2013) Eng. Appl. Artif. Intell. , vol.26 , Issue.1 , pp. 660-668
    • Manuel, M.1    Elias, E.2
  • 23
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • L.J. McGuffin, K. Bryson, and D.T. Jones The PSIPRED protein structure prediction server Bioinformatics 16 4 2000 404 405
    • (2000) Bioinformatics , vol.16 , Issue.4 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 24
    • 33747586510 scopus 로고    scopus 로고
    • Improving the accuracy of protein secondary structure prediction using structural alignment
    • S. Montgomerie, S. Sundararaj, W.J. Gallin, and D.S. Wishart Improving the accuracy of protein secondary structure prediction using structural alignment BMC Bioinform. 7 2006 301
    • (2006) BMC Bioinform. , vol.7 , pp. 301
    • Montgomerie, S.1    Sundararaj, S.2    Gallin, W.J.3    Wishart, D.S.4
  • 25
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 4 1995 536 540
    • (1995) J. Mol. Biol. , vol.247 , Issue.4 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 27
    • 34547127137 scopus 로고    scopus 로고
    • Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information
    • G. Pollastri, A.J. Martin, C. Mooney, and A. Vullo Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information BMC Bioinform. 8 2007 201
    • (2007) BMC Bioinform. , vol.8 , pp. 201
    • Pollastri, G.1    Martin, A.J.2    Mooney, C.3    Vullo, A.4
  • 28
    • 0036467068 scopus 로고    scopus 로고
    • Alignments grow, secondary structure prediction improves
    • D. Przybylski, and B. Rost Alignments grow, secondary structure prediction improves Proteins: Struct.Funct. Bioinform. 46 2 2002 197 205
    • (2002) Proteins: Struct.Funct. Bioinform. , vol.46 , Issue.2 , pp. 197-205
    • Przybylski, D.1    Rost, B.2
  • 30
    • 0028203106 scopus 로고
    • Convergence analysis of canonical genetic algorithms
    • G. Rudolph Convergence analysis of canonical genetic algorithms IEEE Trans. Neural Networks 5 1 1994 96 101
    • (1994) IEEE Trans. Neural Networks , vol.5 , Issue.1 , pp. 96-101
    • Rudolph, G.1
  • 31
    • 25444462754 scopus 로고    scopus 로고
    • An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem
    • A. Shmygelska, and H.H. Hoos An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem BMC Bioinform. 6 1 2005 30
    • (2005) BMC Bioinform. , vol.6 , Issue.1 , pp. 30
    • Shmygelska, A.1    Hoos, H.H.2
  • 33
    • 0003853519 scopus 로고
    • Differential evolution - A simple and efficient adaptive scheme for global optimization over continuous spaces
    • Berkeley, CA
    • Storn, R., Price, K., 1995. Differential Evolution - A Simple and Efficient Adaptive Scheme for Global Optimization Over Continuous Spaces. Technical Report TR-95-012. Berkeley, CA.
    • (1995) Technical Report TR-95-012
    • Storn, R.1    Price, K.2
  • 35
    • 84875133509 scopus 로고    scopus 로고
    • An efficient and robust artificial bee colony algorithm for numerical optimization
    • W. Xiang, and M. An An efficient and robust artificial bee colony algorithm for numerical optimization Comput. Oper. Res. 40 5 2012 1256 1265
    • (2012) Comput. Oper. Res. , vol.40 , Issue.5 , pp. 1256-1265
    • Xiang, W.1    An, M.2
  • 37
    • 49749132014 scopus 로고    scopus 로고
    • Improved prediction of subcellular location for apoptosis proteins by the dual-layer support vector machine
    • X.B. Zhou, C. Chen, Z.C. Li, and X.Y. Zou Improved prediction of subcellular location for apoptosis proteins by the dual-layer support vector machine Amino Acids 35 2 2008 383 388
    • (2008) Amino Acids , vol.35 , Issue.2 , pp. 383-388
    • Zhou, X.B.1    Chen, C.2    Li, Z.C.3    Zou, X.Y.4
  • 38
    • 84877790780 scopus 로고    scopus 로고
    • Analysis of protein folding using a novel hybrid evolutionary algorithm
    • (in Chinese)
    • Y. Zhou, and P. Han Analysis of protein folding using a novel hybrid evolutionary algorithm China J. Bioinform. 8 1 2010 73 75 (in Chinese)
    • (2010) China J. Bioinform. , vol.8 , Issue.1 , pp. 73-75
    • Zhou, Y.1    Han, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.