메뉴 건너뛰기




Volumn 8, Issue 3, 2013, Pages 54-63

Discovering unique, low-energy transition states using evolutionary molecular memetic computing

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL SYSTEMS; COMPUTATIONAL COSTS; EVOLUTIONARY OPERATORS; INDIVIDUAL LEARNING; LANDSCAPE ANALYSIS; MEMETIC ALGORITHMS; SCIENTIFIC COMMUNITY; STATE-OF-THE-ART ALGORITHMS;

EID: 84880546811     PISSN: 1556603X     EISSN: None     Source Type: Journal    
DOI: 10.1109/MCI.2013.2264252     Document Type: Article
Times cited : (9)

References (54)
  • 1
    • 27944507949 scopus 로고    scopus 로고
    • ChemDB: A public database of small molecules and related chemoinformatics resources
    • DOI 10.1093/bioinformatics/bti683
    • J. Chen, S. J. Swamidass, Y. Dou, J. Bruand, and P. Baldi, "ChemDB: A public database of small molecules and related chemoinformatics resources," Bioinformatics, vol. 21, no. 22, pp. 4133-4139, 2005. (Pubitemid 41672103)
    • (2005) Bioinformatics , vol.21 , Issue.22 , pp. 4133-4139
    • Chen, J.1    Swamidass, S.J.2    Dou, Y.3    Bruand, J.4    Baldi, P.5
  • 2
    • 72749127604 scopus 로고    scopus 로고
    • DG-AMMOS: A new tool to generate 3D conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening
    • D. Lagorce, T. Pencheva, B. O. Villoutreix, and M. A. Miteva, "DG-AMMOS: A new tool to generate 3D conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening," BMC Chemical Biol., vol. 9, no. 1, pp. 1-10, 2009.
    • (2009) BMC Chemical Biol. , vol.9 , Issue.1 , pp. 1-10
    • Lagorce, D.1    Pencheva, T.2    Villoutreix, B.O.3    Miteva, M.A.4
  • 3
    • 61349109390 scopus 로고    scopus 로고
    • MED-3DMC: A new tool to generate 3D conformation ensembles of small molecules with a monte carlo sampling of the conformational space
    • O. Sperandio, M. Souaille, F. Delfaud, M. A. Miteva, and B. O. Villoutreix, "MED-3DMC: A new tool to generate 3D conformation ensembles of small molecules with a monte carlo sampling of the conformational space," Eur. J. Med. Chem., vol. 44, no. 4, pp. 1405-1409, 2009.
    • (2009) Eur. J. Med. Chem. , vol.44 , Issue.4 , pp. 1405-1409
    • Sperandio, O.1    Souaille, M.2    Delfaud, F.3    Miteva, M.A.4    Villoutreix, B.O.5
  • 4
    • 77954274184 scopus 로고    scopus 로고
    • Frog2: Efficient 3D conformation ensemble generator for small compounds
    • July
    • M. A. Miteva, F. Guyon, and P. Tufféry, "Frog2: Efficient 3D conformation ensemble generator for small compounds," Nucleic Acids Res., vol. 38, pp. W622-W627, July 2010.
    • (2010) Nucleic Acids Res. , vol.38
    • Miteva, M.A.1    Guyon, F.2    Tufféry, P.3
  • 6
    • 1442282189 scopus 로고    scopus 로고
    • A doubly nudged elastic band method for finding transition states
    • S. A. Trygubenko and D. J. Wales, "A doubly nudged elastic band method for finding transition states," J. Chem. Phys., vol. 120, no. 5, pp. 2082-2094, 2004.
    • (2004) J. Chem. Phys. , vol.120 , Issue.5 , pp. 2082-2094
    • Trygubenko, S.A.1    Wales, D.J.2
  • 7
    • 21644454399 scopus 로고    scopus 로고
    • Finding pathways between distant local minima
    • J. M. Carr, S. A. Trygubenko, and D. J. Wales, "Finding pathways between distant local minima," J. Chem. Phys., vol. 122, no. 23, pp. 234903-234909, 2005.
    • (2005) J. Chem. Phys. , vol.122 , Issue.23 , pp. 234903-234909
    • Carr, J.M.1    Trygubenko, S.A.2    Wales, D.J.3
  • 8
    • 35148901523 scopus 로고    scopus 로고
    • Comparison of double-ended transition state search methods
    • E. S. Koslover, and D. J. Wales, "Comparison of double-ended transition state search methods," J. Chem. Phys., vol. 127, no. 13, pp. 134102-134113, 2007.
    • (2007) J. Chem. Phys. , vol.127 , Issue.13 , pp. 134102-134113
    • Koslover, E.S.1    Wales, D.J.2
  • 9
    • 41949085799 scopus 로고    scopus 로고
    • Optimization methods for finding minimum energy paths
    • D. Sheppard, R. Terrell, and G. Henkelman, "Optimization methods for finding minimum energy paths," J. Chem. Phys., vol. 128, no. 13, pp. 134106-134115, 2008.
    • (2008) J. Chem. Phys. , vol.128 , Issue.13 , pp. 134106-134115
    • Sheppard, D.1    Terrell, R.2    Henkelman, G.3
  • 10
    • 10844224689 scopus 로고    scopus 로고
    • Comparison of methods for finding saddle points without knowledge of the final states
    • DOI 10.1063/1.1809574
    • R. A. Olsen, G. J. Kroes, G. Henkelman, A. Arnaldsson, and H. Jónsson, "Comparison of methods for finding saddle points without knowledge of the final states," J. Chem. Phys., vol. 121, no. 20, pp. 9776-9792, 2004. (Pubitemid 40005747)
    • (2004) Journal of Chemical Physics , vol.121 , Issue.20 , pp. 9776-9792
    • Olsen, R.A.1    Kroes, G.J.2    Henkelman, G.3    Arnaldsson, A.4    Jonsson, H.5
  • 11
    • 0042352697 scopus 로고    scopus 로고
    • A simulated annealing based technique for locating first-order saddle points on multidimensional surfaces and constructing reaction paths: Several model studies
    • PII S0166128097003503
    • P. Chaudhury and S. P. Bhattacharyya, "A simulated annealing based technique for locating first-order saddle points on multidimensional surfaces and constructing reaction paths: Several model studies," J. Mol. Struct.: THEOCHEM, vol. 429, pp. 175-186, Mar. 1998. (Pubitemid 128388590)
    • (1998) Journal of Molecular Structure: THEOCHEM , vol.429 , Issue.1-3 , pp. 175-186
    • Chaudhury, P.1    Bhattacharyya, S.P.2
  • 12
    • 0034158641 scopus 로고    scopus 로고
    • A genetic algorithm based technique for locating first-order saddle point using a gradient-dominated recipe
    • P. Chaudhury, S. P. Bhattacharyya, and W. Quapp, "A genetic algorithm based technique for locating first-order saddle point using a gradient-dominated recipe," Chem. Phys., vol. 253, nos. 2-3, pp. 295-303, 2000.
    • (2000) Chem. Phys. , vol.253 , Issue.2-3 , pp. 295-303
    • Chaudhury, P.1    Bhattacharyya, S.P.2    Quapp, W.3
  • 13
    • 0034340223 scopus 로고    scopus 로고
    • Optimization of transition state structures using genetic algorithms
    • Dec.
    • S. D. Bungay, R. A. Poirier, and R. J. Charron, "Optimization of transition state structures using genetic algorithms," J. Math. Chem., vol. 28, no. 4, pp. 389-401, Dec. 2000.
    • (2000) J. Math. Chem. , vol.28 , Issue.4 , pp. 389-401
    • Bungay, S.D.1    Poirier, R.A.2    Charron, R.J.3
  • 15
    • 84986439201 scopus 로고
    • Optimization of equilibrium geometries and transition structures
    • H. B. Schlegel, "Optimization of equilibrium geometries and transition structures," J. Comput. Chemistry, vol. 3, no. 2, pp. 214-218, 1982.
    • (1982) J. Comput. Chemistry , vol.3 , Issue.2 , pp. 214-218
    • Schlegel, H.B.1
  • 17
    • 2442474238 scopus 로고    scopus 로고
    • Meta-Lamarckian learning in memetic algorithm
    • Y. S. Ong and A. J. Keane, "Meta-Lamarckian learning in memetic algorithm," IEEE Trans. Evol. Comput., vol. 8, no. 2, pp. 99-110, 2004.
    • (2004) IEEE Trans. Evol. Comput. , vol.8 , Issue.2 , pp. 99-110
    • Ong, Y.S.1    Keane, A.J.2
  • 18
    • 77951287415 scopus 로고    scopus 로고
    • Lamarckian memetic algorithms: Local optimum and connectivity structure analysis
    • M. N. Le, Y. S. Ong, Y. Jin, and B. Sendhoff, "Lamarckian memetic algorithms: Local optimum and connectivity structure analysis," Memetic Comput., vol. 1, no. 3, pp. 175-190, 2009.
    • (2009) Memetic Comput. , vol.1 , Issue.3 , pp. 175-190
    • Le, M.N.1    Ong, Y.S.2    Jin, Y.3    Sendhoff, B.4
  • 19
    • 71749089181 scopus 로고    scopus 로고
    • An evolutionary memetic algorithm for rule extraction
    • J. H. Ang, K. C. Tan, and A. A. Mamun, "An evolutionary memetic algorithm for rule extraction," Expert Syst. Applicat., vol. 37, no. 2, pp. 1302-1315, 2010.
    • (2010) Expert Syst. Applicat. , vol.37 , Issue.2 , pp. 1302-1315
    • Ang, J.H.1    Tan, K.C.2    Mamun, A.A.3
  • 20
    • 0035958744 scopus 로고    scopus 로고
    • Statistical thermodynamics: Taking a walk on a landscape
    • C. L. Brooks III, J. N. Onuchic, and D. J. Wales, "Statistical thermodynamics. Taking a walk on a landscape," Science, vol. 293, no. 5530, pp. 612-613, 2001. (Pubitemid 32728648)
    • (2001) Science , vol.293 , Issue.5530 , pp. 612-613
    • Brooks III, C.L.1    Onuchic, J.N.2    Wales, D.J.3
  • 22
    • 77953082750 scopus 로고    scopus 로고
    • Discovering unique, low-energy pure water isomers: Memetic exploration, optimization, and landscape analysis
    • H. Soh, Y. S. Ong, Q. C. Nguyen, Q. H. Nguyen, M. S. Habibullah, T. Hung, and J. L. Kuo, "Discovering unique, low-energy pure water isomers: Memetic exploration, optimization, and landscape analysis," IEEE Trans. Evol. Comput., vol. 14, no. 3, pp. 419-437, 2010.
    • (2010) IEEE Trans. Evol. Comput. , vol.14 , Issue.3 , pp. 419-437
    • Soh, H.1    Ong, Y.S.2    Nguyen, Q.C.3    Nguyen, Q.H.4    Habibullah, M.S.5    Hung, T.6    Kuo, J.L.7
  • 24
    • 78649510317 scopus 로고    scopus 로고
    • Complementing ultrafast shape recognition with an optical isomerism descriptor
    • T. Zhou, K. Laf leur, and A. Caf lisch, "Complementing ultrafast shape recognition with an optical isomerism descriptor," J. Mol. Graph. Model., vol. 29, no. 3, pp. 443-449, 2010.
    • (2010) J. Mol. Graph. Model. , vol.29 , Issue.3 , pp. 443-449
    • Zhou, T.1    Lafleur, K.2    Caflisch, A.3
  • 25
    • 78650643212 scopus 로고    scopus 로고
    • Ultrafast shape recognition: Method and applications
    • P. J. Ballester, "Ultrafast shape recognition: Method and applications," Future Med. Chem., vol. 3, no. 1, pp. 65-78, 2011.
    • (2011) Future Med. Chem. , vol.3 , Issue.1 , pp. 65-78
    • Ballester, P.J.1
  • 26
    • 0000507524 scopus 로고
    • Ab initio transition state theory calculations of the reaction rate for OH+CH4"H2O+CH3
    • T. N. Truong, and D. G. Truhlar, "Ab initio transition state theory calculations of the reaction rate for OH+CH4"H2O+CH3," J. Chem. Phys., vol. 93, no. 3, pp. 1761-1769, 1990.
    • (1990) J. Chem. Phys. , vol.93 , Issue.3 , pp. 1761-1769
    • Truong, T.N.1    Truhlar, D.G.2
  • 27
    • 0011690680 scopus 로고    scopus 로고
    • Methods for finding saddle points and minimum energy paths
    • G. Henkelman and G. Jóhannesson, "Methods for finding saddle points and minimum energy paths," Prog. Theor. Chem. Phys., vol. 5, pp. 269-302, 2002.
    • (2002) Prog. Theor. Chem. Phys. , vol.5 , pp. 269-302
    • Henkelman, G.1    Jóhannesson, G.2
  • 28
    • 0003603223 scopus 로고
    • On evolution, search, optimization, genetic algorithms, and martial arts: Towards memetic algorithms
    • Pasadena, CA, Tech. Rep. C3P-826
    • P. Moscato, "On evolution, search, optimization, genetic algorithms, and martial arts: Towards memetic algorithms," in Caltech Concurrent Computation Program, California Inst. Technol., Pasadena, CA, Tech. Rep. C3P-826, 1989.
    • (1989) Caltech Concurrent Computation Program, California Inst. Technol.
    • Moscato, P.1
  • 30
    • 55749089341 scopus 로고    scopus 로고
    • A real-coded niching memetic algorithm for continuous multimodal function optimization
    • J. E. Vitela and O. Castanos, "A real-coded niching memetic algorithm for continuous multimodal function optimization," in Proc. IEEE Congr. Evolutionary Computation, 2008, pp. 2170-2177.
    • (2008) Proc. IEEE Congr. Evolutionary Computation , pp. 2170-2177
    • Vitela, J.E.1    Castanos, O.2
  • 31
    • 77951278725 scopus 로고    scopus 로고
    • Memetic computation-Past, present, & future
    • Y. S. Ong, M. H. Lim, and X. S. Chen, "Memetic computation-Past, present, & future," IEEE Comput. Intell. Mag., vol. 5, no. 2, pp. 24-36, 2010.
    • (2010) IEEE Comput. Intell. Mag. , vol.5 , Issue.2 , pp. 24-36
    • Ong, Y.S.1    Lim, M.H.2    Chen, X.S.3
  • 32
    • 80054688019 scopus 로고    scopus 로고
    • A multi-facet survey on memetic computation
    • X. S. Chen, Y. S. Ong, M. H. Lim, and K. C. Tan, "A multi-facet survey on memetic computation," IEEE Trans. Evol. Comput., vol. 15, no. 5, pp. 591-607, 2011.
    • (2011) IEEE Trans. Evol. Comput. , vol.15 , Issue.5 , pp. 591-607
    • Chen, X.S.1    Ong, Y.S.2    Lim, M.H.3    Tan, K.C.4
  • 33
    • 79955605067 scopus 로고    scopus 로고
    • A two-stage hybrid memetic algorithm for multiobjective job shop scheduling
    • H. C. Cheng, T. C. Chiang, and L. C. Fu, "A two-stage hybrid memetic algorithm for multiobjective job shop scheduling," Expert Syst. Applicat., vol. 38, no. 9, pp. 10983-10998, 2011.
    • (2011) Expert Syst. Applicat. , vol.38 , Issue.9 , pp. 10983-10998
    • Cheng, H.C.1    Chiang, T.C.2    Fu, L.C.3
  • 35
    • 84880531735 scopus 로고    scopus 로고
    • A framework for finding robust optimal solutions over time
    • to be published
    • Y. Jin, K. Tang, X. Yu, B. Sendhoff, and X. Yao, "A framework for finding robust optimal solutions over time," Memetic Comput., to be published.
    • Memetic Comput
    • Jin, Y.1    Tang, K.2    Yu, X.3    Sendhoff, B.4    Yao, X.5
  • 37
    • 79959382418 scopus 로고    scopus 로고
    • Memetic informed evolutionary optimization via data mining
    • J. Y. Chia, C. K. Goh, K. C. Tan, and V. A. Shim, "Memetic informed evolutionary optimization via data mining," Memetic Comput., vol. 3, no. 2, pp. 73-87, 2011.
    • (2011) Memetic Comput. , vol.3 , Issue.2 , pp. 73-87
    • Chia, J.Y.1    Goh, C.K.2    Tan, K.C.3    Shim, V.A.4
  • 38
    • 80054957568 scopus 로고    scopus 로고
    • Medical image registration using evolutionary computation: An experimental survey
    • S. Damas, O. Cordón, and J. Santamaría, "Medical image registration using evolutionary computation: An experimental survey," IEEE Comput. Intell. Mag., vol. 6, no. 4, pp. 26-42, 2011.
    • (2011) IEEE Comput. Intell. Mag. , vol.6 , Issue.4 , pp. 26-42
    • Damas, S.1    Cordón, O.2    Santamaría, J.3
  • 39
    • 78951471310 scopus 로고    scopus 로고
    • Autonomous self-reconfiguration of modular robots by evolving a hierarchical mechanochemical model
    • Y. Meng, Y. Zheng, and Y. Jin, "Autonomous self-reconfiguration of modular robots by evolving a hierarchical mechanochemical model," IEEE Comput. Intell. Mag., vol. 6, no. 1, pp. 43-54, 2011.
    • (2011) IEEE Comput. Intell. Mag. , vol.6 , Issue.1 , pp. 43-54
    • Meng, Y.1    Zheng, Y.2    Jin, Y.3
  • 40
    • 79960559355 scopus 로고    scopus 로고
    • Evolutionary algorithms for solving multi-objective travelling salesman problems
    • V. A. Shim, K. C. Tan, J. Y. Chia, and J. K. Chong, "Evolutionary algorithms for solving multi-objective travelling salesman problems," Flexible Services Manuf., vol. 23, no. 2, pp. 207-241, 2011.
    • (2011) Flexible Services Manuf. , vol.23 , Issue.2 , pp. 207-241
    • Shim, V.A.1    Tan, K.C.2    Chia, J.Y.3    Chong, J.K.4
  • 41
    • 84856365876 scopus 로고    scopus 로고
    • A unified framework for symbiosis of evolutionary mechanisms with application to water clusters potential model design
    • M. N. Le, Y. S. Ong, Y. Jin, and B. Sendhoff, "A unified framework for symbiosis of evolutionary mechanisms with application to water clusters potential model design," IEEE Comput. Intell. Mag., vol. 7, no. 1, pp. 20-35, 2012.
    • (2012) IEEE Comput. Intell. Mag. , vol.7 , Issue.1 , pp. 20-35
    • Le, M.N.1    Ong, Y.S.2    Jin, Y.3    Sendhoff, B.4
  • 42
    • 84870253684 scopus 로고    scopus 로고
    • A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules
    • M. M. H. Ellabaan, S. D. Handoko, Y. S. Ong, C. K. Kwoh, S. Bahnassy, F. Elassawy, and H. Y. Man, "A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules," Comput. Math. Applicat., vol. 64, no. 12, pp. 3792-3804, 2012.
    • (2012) Comput. Math. Applicat. , vol.64 , Issue.12 , pp. 3792-3804
    • Ellabaan, M.M.H.1    Handoko, S.D.2    Ong, Y.S.3    Kwoh, C.K.4    Bahnassy, S.5    Elassawy, F.6    Man, H.Y.7
  • 43
    • 84865007653 scopus 로고    scopus 로고
    • Evolutionary discovery of transition states in water clusters
    • M. M. H. Ellabaan, Y. S. Ong, Q. C. Nguyen, and J. L. Kuo, "Evolutionary discovery of transition states in water clusters," J. Theor. Comput. Chem., vol. 11, no. 5, pp. 965-995, 2012.
    • (2012) J. Theor. Comput. Chem. , vol.11 , Issue.5 , pp. 965-995
    • Ellabaan, M.M.H.1    Ong, Y.S.2    Nguyen, Q.C.3    Kuo, J.L.4
  • 44
    • 84865040656 scopus 로고    scopus 로고
    • Experiences on memetic computation for locating transition states in biochemical applications
    • M. M. H. Ellabaan and Y. S. Ong, "Experiences on memetic computation for locating transition states in biochemical applications," in Proc. Genetic Evolutionary Computation Conf., 2012, pp. 623-624.
    • (2012) Proc. Genetic Evolutionary Computation Conf. , pp. 623-624
    • Ellabaan, M.M.H.1    Ong, Y.S.2
  • 45
    • 84880515157 scopus 로고    scopus 로고
    • Evolving connectivity between genetic oscillators and switches using evolutionary algorithms
    • Biol., to be published
    • S. A. Thomas and Y. Jin, "Evolving connectivity between genetic oscillators and switches using evolutionary algorithms," J. Bioinform. Comput. Biol., to be published.
    • J. Bioinform. Comput
    • Thomas, S.A.1    Jin, Y.2
  • 46
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • W. Kabsch, "A solution for the best rotation to relate two sets of vectors," Acta Crystallogr., vol. 32, no. 5, pp. 922-923, 1976.
    • (1976) Acta Crystallogr. , vol.32 , Issue.5 , pp. 922-923
    • Kabsch, W.1
  • 48
    • 84871374782 scopus 로고    scopus 로고
    • Multi-modal valleyadaptive memetic algorithm for efficient discovery of first-order saddle points
    • M. M. H. Ellabaan, X. S. Chen, and Q. H. Nguyen, "Multi-modal valleyadaptive memetic algorithm for efficient discovery of first-order saddle points," in Proc. 9th Int. Conf. Simulated Evolution Learning, 2012, pp. 83-92.
    • (2012) Proc. 9th Int. Conf. Simulated Evolution Learning , pp. 83-92
    • Ellabaan, M.M.H.1    Chen, X.S.2    Nguyen, Q.H.3
  • 49
    • 70349615421 scopus 로고    scopus 로고
    • Locating and characterizing the stationary points of the extended rosenbrock function
    • S. Kok and C. Sandrock, "Locating and characterizing the stationary points of the extended rosenbrock function," Evol. Comput., vol. 17, no. 3, pp. 437-453, 2009.
    • (2009) Evol. Comput. , vol.17 , Issue.3 , pp. 437-453
    • Kok, S.1    Sandrock, C.2
  • 50
    • 78149298732 scopus 로고    scopus 로고
    • Long-range migration of a water molecule to catalyze a tautomerization in photoionization of the hydrated formamide cluster
    • S. Maeda, Y. Matsuda, S. Mizutani, A. Fujii, and K. Ohno, "Long-range migration of a water molecule to catalyze a tautomerization in photoionization of the hydrated formamide cluster," J. Phys. Chem. A, vol. 114, no. 44, pp. 11896-11899, 2010.
    • (2010) J. Phys. Chem. A , vol.114 , Issue.44 , pp. 11896-11899
    • Maeda, S.1    Matsuda, Y.2    Mizutani, S.3    Fujii, A.4    Ohno, K.5
  • 53
    • 77957572225 scopus 로고    scopus 로고
    • Feasibility structure modeling: An effective chaperone for constrained memetic algorithms
    • S. D. Handoko, C. K. Kwoh, and Y. S. Ong, "Feasibility structure modeling: An effective chaperone for constrained memetic algorithms," IEEE Trans. Evol. Comput., vol. 14, no. 5, pp. 740-758, 2010.
    • (2010) IEEE Trans. Evol. Comput. , vol.14 , Issue.5 , pp. 740-758
    • Handoko, S.D.1    Kwoh, C.K.2    Ong, Y.S.3
  • 54
    • 80051996131 scopus 로고    scopus 로고
    • Classificationassisted memetic algorithms for solving optimization problems with restricted equality constraint function mapping
    • S. D. Handoko, C. K. Kwoh, Y. S. Ong, and J. Chan, " Classificationassisted memetic algorithms for solving optimization problems with restricted equality constraint function mapping," in Proc. 2011 IEEE Congr. Evolutionary Computation, 2011, pp. 1209-1216.
    • (2011) Proc. 2011 IEEE Congr. Evolutionary Computation , pp. 1209-1216
    • Handoko, S.D.1    Kwoh, C.K.2    Ong, Y.S.3    Chan, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.