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Volumn 6, Issue , 2005, Pages

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem

Author keywords

[No Author keywords available]

Indexed keywords

ANT COLONY OPTIMISATION; COMBINATORIAL PROBLEM; COMPUTATIONAL MOLECULAR BIOLOGY; HYDROPHOBIC-POLAR MODEL; HYDROPHOBIC-POLAR PROTEINS; PROTEIN FOLDING PROBLEM; STATE-OF-THE-ART ALGORITHMS; STATE-OF-THE-ART METHODS;

EID: 25444462754     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-30     Document Type: Article
Times cited : (231)

References (45)
  • 1
    • 0004061426 scopus 로고
    • Positive feedback as a search strategy
    • Tech. rep. 91-016 Dip Elettronica, Politecnico di Milano, Italy
    • Dorigo M, Maniezzo V, Colorni A: Positive feedback as a search strategy. Tech rep., 91-016, Dip Elettronica, Politecnico di Milano, Italy 1991.
    • (1991)
    • Dorigo, M.1    Maniezzo, V.2    Colorni, A.3
  • 3
    • 0004033139 scopus 로고    scopus 로고
    • New Ideas in Optimization
    • Edited by: Corne D, Dorigo M, Glover F. McGraw-Hill
    • Dorigo M, Di Caro G: New Ideas in Optimization. In New Ideas in Optimization Edited by: Corne D, Dorigo M, Glover F. McGraw-Hill; 1999.
    • (1999) New Ideas in Optimization
    • Dorigo, M.1    Di Caro, G.2
  • 7
    • 4143144886 scopus 로고    scopus 로고
    • An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem
    • LNCS 2671 Springer Verlag
    • Shmygelska A, Hoos HH: An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem. In Proc of the 16th Canadian Conference on Artificial Intelligence, LNCS 2671 Springer Verlag; 2003:400-17.
    • (2003) Proc. of the 16th Canadian Conference on Artificial Intelligence , pp. 400-417
    • Shmygelska, A.1    Hoos, H.H.2
  • 8
    • 0027690211 scopus 로고
    • Finding the lowest Free-Energy Conformation of a protein is an NP-hard problem - Proof and Implications
    • Unger R, Moult J: Finding the lowest Free-Energy Conformation of a protein is an NP-hard problem - Proof and Implications. Bull Math Biol 1993, 55(6):1183-1198.
    • (1993) Bull. Math. Biol. , vol.55 , Issue.6 , pp. 1183-1198
    • Unger, R.1    Moult, J.2
  • 9
    • 0024750637 scopus 로고
    • Lattice statistical mechanics model of the conformation and sequence space of proteins
    • Lau KF, Dill KA: lattice statistical mechanics model of the conformation and sequence space of proteins. Macromolecules 1989, 22:3986-3997.
    • (1989) Macromolecules , vol.22 , pp. 3986-3997
    • Lau, K.F.1    Dill, K.A.2
  • 10
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein structures
    • Richards FM: Areas, volumes, packing, and protein structures. Annu Rev Biophys Bioeng 1977, 6:151-176.
    • (1977) Annu. Rev. Biophys. Bioeng. , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 13
    • 0011484346 scopus 로고
    • A standard GA approach to native protein conformation prediction
    • Morgan Kaufmann Publishers
    • Patton AWP, Goldman E: A standard GA approach to native protein conformation prediction. In Proc of the 6th Intl Conf Genetic Algorithms Morgan Kaufmann Publishers; 1995:574-581.
    • (1995) Proc. of the 6th Intl. Conf. Genetic Algorithms , pp. 574-581
    • Patton, A.W.P.1    Goldman, E.2
  • 14
    • 0027245418 scopus 로고
    • Genetic algorithms for protein folding simulations
    • Unger R, Moult J: Genetic algorithms for protein folding simulations. J of Mol Biol 1993, 231:75-81.
    • (1993) J. of Mol. Biol. , vol.231 , pp. 75-81
    • Unger, R.1    Moult, J.2
  • 15
    • 1642289227 scopus 로고
    • A genetic algorithm for three dimensional protein folding simulations
    • Morgan Kaufmann Publishers
    • Unger R, Moult J: A genetic algorithm for three dimensional protein folding simulations. In Proc of the 5th Intl Conf on Genetic Algorithms Morgan Kaufmann Publishers; 1993:581-588.
    • (1993) Proc. of the 5th Intl. Conf. on Genetic Algorithms , pp. 581-588
    • Unger, R.1    Moult, J.2
  • 17
    • 84885681358 scopus 로고    scopus 로고
    • Multi-Self-Overlap Ensemble for protein folding: Ground state search and thermodynamics
    • Chikenji G, Kikuchi M, Iba Y: Multi-Self-Overlap Ensemble for protein folding: ground state search and thermodynamics. Condensed Materials Archive 1999:27.
    • (1999) Condensed Materials Archive , pp. 27
    • Chikenji, G.1    Kikuchi, M.2    Iba, Y.3
  • 18
    • 0037258333 scopus 로고    scopus 로고
    • Growth Algorithm for Lattice Heteropolymers at Low Temperatures
    • Hsu HP, Mehra V, Nadler W, Grassberger P: Growth Algorithm for Lattice Heteropolymers at Low Temperatures. J Chem Phys 2003, 118:444-51.
    • (2003) J. Chem. Phys. , vol.118 , pp. 444-451
    • Hsu, H.P.1    Mehra, V.2    Nadler, W.3    Grassberger, P.4
  • 19
    • 0035880733 scopus 로고    scopus 로고
    • Evolutionary Monte Carlo for protein folding simulations
    • Liang F, Wong WH: Evolutionary Monte Carlo for protein folding simulations. J Chem Phys 2001, 115(7):3374-3380.
    • (2001) J. Chem. Phys. , vol.115 , Issue.7 , pp. 3374-3380
    • Liang, F.1    Wong, W.H.2
  • 20
    • 0000669827 scopus 로고
    • Monte Carlo simulation of folding transitions of simple model proteins using a chain growth algorithm
    • O'Toole EM, Panagiotopoulos AZ: Monte Carlo simulation of folding transitions of simple model proteins using a chain growth algorithm. J Chem Phys 1992, 97(11):8644-8652.
    • (1992) J. Chem. Phys. , vol.97 , Issue.11 , pp. 8644-8652
    • O'Toole, E.M.1    Panagiotopoulos, A.Z.2
  • 21
    • 0001437596 scopus 로고    scopus 로고
    • A dynamic Monte Carlo algorithm for exploration of dense conformational spaces in heteropolymers
    • Ramakrishnan R, Ramachandran B, Pekny JF: A dynamic Monte Carlo algorithm for exploration of dense conformational spaces in heteropolymers. J Chem Phys 1997, 106(6):2418-2424.
    • (1997) J. Chem. Phys. , vol.106 , Issue.6 , pp. 2418-2424
    • Ramakrishnan, R.1    Ramachandran, B.2    Pekny, J.F.3
  • 24
    • 0030034935 scopus 로고    scopus 로고
    • Contact interactions method: A new algorithm for protein folding simulations
    • Toma L, Toma S: Contact interactions method: A new algorithm for protein folding simulations. Protein Sci 1996, 5:147-153.
    • (1996) Protein Sci. , vol.5 , pp. 147-153
    • Toma, L.1    Toma, S.2
  • 25
    • 0029909775 scopus 로고    scopus 로고
    • A fast conformational search strategy for finding low energy structures of model proteins
    • Beutler T, Dill K: A fast conformational search strategy for finding low energy structures of model proteins. Protein Sci 1996, 5:2037-2043.
    • (1996) Protein Sci. , vol.5 , pp. 2037-2043
    • Beutler, T.1    Dill, K.2
  • 26
    • 0028950075 scopus 로고
    • Forces of Tertiary Structural Organization in Globular Proteins
    • Yue K, Dill KA: Forces of Tertiary Structural Organization in Globular Proteins. Proc Natl Acad Sci USA 1995, 92:146-150.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 146-150
    • Yue, K.1    Dill, K.A.2
  • 27
    • 0348155923 scopus 로고    scopus 로고
    • A Constraint-Based Approach to Structure Prediction for Simplified Protein Models that Outperforms Other Existing Methods
    • Backofen R, Will S: A Constraint-Based Approach to Structure Prediction for Simplified Protein Models that Outperforms Other Existing Methods. Proc XIX Intl Conf on Logic Programming 2003:49-71.
    • (2003) Proc. XIX Intl. Conf. on Logic Programming , pp. 49-71
    • Backofen, R.1    Will, S.2
  • 28
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in MC free energy estimation: Umbrella sampling
    • Torrie GM, Valleau JP: Nonphysical sampling distributions in MC free energy estimation: Umbrella sampling. J Comput Phys 1977, 23:187-199.
    • (1977) J. Comput. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 29
    • 0034275016 scopus 로고    scopus 로고
    • Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures
    • Gront D, Kolinski A, Skolnick J: Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures. J Chem Phys 2000, 113(12):5065-5071.
    • (2000) J. Chem. Phys. , vol.113 , Issue.12 , pp. 5065-5071
    • Gront, D.1    Kolinski, A.2    Skolnick, J.3
  • 30
    • 0037961507 scopus 로고    scopus 로고
    • Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test
    • Mitsutake A, Sugita Y, Okamoto Y: Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test. J Chem Phys 2003, 118(14):6664-6675.
    • (2003) J. Chem. Phys. , vol.118 , Issue.14 , pp. 6664-6675
    • Mitsutake, A.1    Sugita, Y.2    Okamoto, Y.3
  • 31
    • 4243613377 scopus 로고
    • Multicanonical ensemble: A new approach to simulate first-order phase transitions
    • Berg BA, Neuhaus T: Multicanonical ensemble: A new approach to simulate first-order phase transitions. Phys Rev Lett 1992, 68:9-12.
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 9-12
    • Berg, B.A.1    Neuhaus, T.2
  • 32
    • 0002501593 scopus 로고    scopus 로고
    • Dynamic-parameter algorithms for protein folding
    • Edited by: Grassberger P, Barkema GT, Nadler W,. World Scientific, Singapore
    • Irbäck A: Dynamic-parameter algorithms for protein folding. In Monte Carlo Approach to Biopolymers and Protein Folding Edited by: Grassberger P, Barkema GT, Nadler W,. World Scientific, Singapore; 1998:98-109.
    • (1998) Monte Carlo Approach to Biopolymers and Protein Folding , pp. 98-109
    • Irbäck, A.1
  • 34
    • 42749103620 scopus 로고    scopus 로고
    • Growth-based Optimisation Algorithm for Lattice Heteropolymers
    • Hsu HP, Mehra V, Nadler W, Grassberger P: Growth-based Optimisation Algorithm for Lattice Heteropolymers. Phys Rev E 2003, 68:021113-1-021113-4.
    • (2003) Phys. Rev. E , vol.68
    • Hsu, H.P.1    Mehra, V.2    Nadler, W.3    Grassberger, P.4
  • 35
    • 0036205910 scopus 로고    scopus 로고
    • Comparative Genomics using Data Mining tools
    • Nandi T, B-Rao C, Ramachandran S: Comparative Genomics using Data Mining tools. J Bioscience 2002, 27:15-25.
    • (2002) J. Bioscience , vol.27 , pp. 15-25
    • Nandi, T.1    B-Rao, C.2    Ramachandran, S.3
  • 36
    • 0029119568 scopus 로고
    • RASMOL - Biomolecular Graphics for All
    • Sayle R, Milner-White EJ: RASMOL - Biomolecular Graphics for All. Trends Biochem Sci 1995, 20(9):374-376.
    • (1995) Trends Biochem. Sci. , vol.20 , Issue.9 , pp. 374-376
    • Sayle, R.1    Milner-White, E.J.2
  • 37
    • 84874652813 scopus 로고
    • Protein Folding W H Freeman and Company
    • Creighton TE: Protein Folding W H Freeman and Company; 1992.
    • (1992)
    • Creighton, T.E.1
  • 38
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domainproteins
    • Plaxco KW, Simons KT, Baker D: Contact order, transition state placement and the refolding rates of single domainproteins. J Mol Biol 1998, 277:985-994.
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 40
    • 0028270634 scopus 로고
    • Kinetics of protein folding - A lattice model study of the requirements for folding tothe native state
    • Sali A, Shakhnovich E, Karplus M: Kinetics of protein folding - A lattice model study of the requirements for folding tothe native state. J Mol Biol 1994, 235:1614-1636.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1614-1636
    • Sali, A.1    Shakhnovich, E.2    Karplus, M.3
  • 44
    • 84874648403 scopus 로고    scopus 로고
    • HP Benchmarks
    • HP Benchmarks http://www.cs.sandia.gov/tech_reports/compbio/tortilla-hp-benchmarks.html
  • 45
    • 0142045029 scopus 로고    scopus 로고
    • Improving Genetic Algorithms for Protein Folding simulations by systematic crossover
    • Konig R, Dandekar T: Improving Genetic Algorithms for Protein Folding simulations by systematic crossover. Biosystems 1999, 50:17-25.
    • (1999) Biosystems , vol.50 , pp. 17-25
    • Konig, R.1    Dandekar, T.2


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