메뉴 건너뛰기




Volumn 151, Issue 2, 2003, Pages 121-140

A new class of hybrid global optimization algorithms for peptide structure prediction: Integrated hybrids

Author keywords

Deterministic global optimization; Hybrid global optimization; Protein folding; Stochastic global optimization; Tertiary structure prediction

Indexed keywords

ANNEALING; COMPUTATIONAL METHODS; GLOBAL OPTIMIZATION; NONLINEAR PROGRAMMING; PROTEINS; RANDOM PROCESSES;

EID: 0037445044     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0010-4655(02)00735-X     Document Type: Article
Times cited : (37)

References (32)
  • 1
    • 0032552250 scopus 로고    scopus 로고
    • A global optimization method, αBB, for general twice-differential constrained npls. I. Theoretical advances
    • Adjiman C., Androulakis I., Floudas C.A. A global optimization method, αBB, for general twice-differential constrained npls. I. Theoretical advances. Comput. Chem. Engrg. 22:1998;1137-1158.
    • (1998) Comput. Chem. Engrg. , vol.22 , pp. 1137-1158
    • Adjiman, C.1    Androulakis, I.2    Floudas, C.A.3
  • 2
    • 0032552252 scopus 로고    scopus 로고
    • A global optimization method, αBB, for general twice-differentiable constrained nlps. II. Implementation and computational results
    • Adjiman C., Androulakis I., Floudas C.A. A global optimization method, αBB, for general twice-differentiable constrained nlps. II. Implementation and computational results. Comput. Chem. Engrg. 22:1998;1159-1179.
    • (1998) Comput. Chem. Engrg. , vol.22 , pp. 1159-1179
    • Adjiman, C.1    Androulakis, I.2    Floudas, C.A.3
  • 3
    • 0034282316 scopus 로고    scopus 로고
    • Global optimization of mixed-integer nonlinear problems
    • Adjiman C., Androulakis I., Floudas C.A. Global optimization of mixed-integer nonlinear problems. AiChE J. 46:2000;1769-1797.
    • (2000) AiChE J. , vol.46 , pp. 1769-1797
    • Adjiman, C.1    Androulakis, I.2    Floudas, C.A.3
  • 4
    • 0000292903 scopus 로고    scopus 로고
    • Predicting peptide structures using nmr data and deterministic global optimization
    • Klepeis J.L., Floudas C.A., Morikis D., Lambris J. Predicting peptide structures using nmr data and deterministic global optimization. J. Comput. Chem. 20:1999;1354-1370.
    • (1999) J. Comput. Chem. , vol.20 , pp. 1354-1370
    • Klepeis, J.L.1    Floudas, C.A.2    Morikis, D.3    Lambris, J.4
  • 5
    • 0000812896 scopus 로고    scopus 로고
    • Free energy calculations for peptides via deterministic global optimization
    • Klepeis J.L., Floudas C.A. Free energy calculations for peptides via deterministic global optimization. J. Chem. Phys. 110:1999;7491-7512.
    • (1999) J. Chem. Phys. , vol.110 , pp. 7491-7512
    • Klepeis, J.L.1    Floudas, C.A.2
  • 6
    • 0001352857 scopus 로고    scopus 로고
    • Predicting solvated peptide conformations via global minimization of energetic atom-to-atom interations
    • Klepeis J.L., Androulakis I., Ierapetritou M., Floudas C.A. Predicting solvated peptide conformations via global minimization of energetic atom-to-atom interations. Comput. Chem. Engrg. 22:1998;765-788.
    • (1998) Comput. Chem. Engrg. , vol.22 , pp. 765-788
    • Klepeis, J.L.1    Androulakis, I.2    Ierapetritou, M.3    Floudas, C.A.4
  • 8
    • 78751536855 scopus 로고    scopus 로고
    • Deterministic global optimization and ab initio approaches for the structure prediction of polypeptides, dynamics of protein folding and protein-protein interaction
    • Wiley
    • Klepeis J.L., Schafroth H.D., Westerberg K.M., Floudas C.A. Deterministic global optimization and ab initio approaches for the structure prediction of polypeptides, dynamics of protein folding and protein-protein interaction. Advances in Chemical Physics. 120:2002;254-457 Wiley.
    • (2002) Advances in Chemical Physics , vol.120 , pp. 254-457
    • Klepeis, J.L.1    Schafroth, H.D.2    Westerberg, K.M.3    Floudas, C.A.4
  • 9
    • 0032146482 scopus 로고    scopus 로고
    • Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing
    • Lee J., Scheraga H., Rackovsky S. Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. Biopolymers. 46:1998;103-115.
    • (1998) Biopolymers , vol.46 , pp. 103-115
    • Lee, J.1    Scheraga, H.2    Rackovsky, S.3
  • 10
    • 0001176785 scopus 로고    scopus 로고
    • New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
    • Lee J., Scheraga H., Rackovsky S. New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. J. Comp. Chem. 18:1997;1222-1232.
    • (1997) J. Comp. Chem. , vol.18 , pp. 1222-1232
    • Lee, J.1    Scheraga, H.2    Rackovsky, S.3
  • 11
    • 0000542451 scopus 로고    scopus 로고
    • Conformational space annealing by parallel computations: Extensive conformational search of met-enkephalin and the 20-residue membrane-bound portion of melittin
    • Lee J., Scheraga H. Conformational space annealing by parallel computations: Extensive conformational search of met-enkephalin and the 20-residue membrane-bound portion of melittin. Intl. J. Quantum Chem. 75:1999;255-265.
    • (1999) Intl. J. Quantum Chem. , vol.75 , pp. 255-265
    • Lee, J.1    Scheraga, H.2
  • 12
    • 0032146488 scopus 로고    scopus 로고
    • New developments of the electrostatically driven Monte Carlo method: Tests on the membrane-bound portion of melittin
    • Ripoll D., Liwo A., Scheraga H. New developments of the electrostatically driven Monte Carlo method: Tests on the membrane-bound portion of melittin. Biopolymers. 46:1998;117-126.
    • (1998) Biopolymers , vol.46 , pp. 117-126
    • Ripoll, D.1    Liwo, A.2    Scheraga, H.3
  • 14
    • 67349189383 scopus 로고
    • The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain
    • Anfinsen C., Haber E., Sela M., White F. Jr. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc. Natl. Acad. Sci. USA. 47:1961;1309-1314.
    • (1961) Proc. Natl. Acad. Sci. USA , vol.47 , pp. 1309-1314
    • Anfinsen, C.1    Haber, E.2    Sela, M.3    White F., Jr.4
  • 15
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen C. Principles that govern the folding of protein chains. Science. 181:1973;223-229.
    • (1973) Science , vol.181 , pp. 223-229
    • Anfinsen, C.1
  • 18
    • 84988053694 scopus 로고
    • An all-atom force field for simulations of proteins and nucleic acids
    • Weiner S., Kollman P., Nguyen D., Case D. An all-atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7:1986;230-252.
    • (1986) J. Comp. Chem. , vol.7 , pp. 230-252
    • Weiner, S.1    Kollman, P.2    Nguyen, D.3    Case, D.4
  • 20
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ecepp/3 algorithm with application to proline-containing peptides
    • Nemethy G., Gibson K., Palmer K., Yoon C., Paterlini G., Zagari A., Rumsey S., Scharaga H. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ecepp/3 algorithm with application to proline-containing peptides. J. Phys. Chem. 96:1992;6472-6484.
    • (1992) J. Phys. Chem. , vol.96 , pp. 6472-6484
    • Nemethy, G.1    Gibson, K.2    Palmer, K.3    Yoon, C.4    Paterlini, G.5    Zagari, A.6    Rumsey, S.7    Scharaga, H.8
  • 21
    • 0021095856 scopus 로고
    • Protein folding by restrained energy minimization and molecular dynamics
    • Levitt M. Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol. 170:1983;723-764.
    • (1983) J. Mol. Biol. , vol.170 , pp. 723-764
    • Levitt, M.1
  • 23
    • 0024843595 scopus 로고
    • Molecular mechanics: The mm3 force field for hydrocarbons. 2: Vibrational frequencies and thermodynamics
    • Lii J.-H., Allinger N. Molecular mechanics: The mm3 force field for hydrocarbons. 2: Vibrational frequencies and thermodynamics. J. Amer. Chem. Soc. 111:1989;8566-8575.
    • (1989) J. Amer. Chem. Soc. , vol.111 , pp. 8566-8575
    • Lii, J.-H.1    Allinger, N.2
  • 24
    • 0024804228 scopus 로고
    • Molecular mechanics: The mm3 force field for hydrocarbons. 3: The van der Waals potentials and crystal data for aliphatic and aromatic hydrocarbons
    • Lii J.-H., Allinger N. Molecular mechanics: The mm3 force field for hydrocarbons. 3: The van der Waals potentials and crystal data for aliphatic and aromatic hydrocarbons. J. Amer. Chem. Soc. 111:1989;8576-8582.
    • (1989) J. Amer. Chem. Soc. , vol.111 , pp. 8576-8582
    • Lii, J.-H.1    Allinger, N.2
  • 25
    • 0001643360 scopus 로고
    • Structure and free energy of complex thermodynamic systems
    • Li Z., Scheraga H. Structure and free energy of complex thermodynamic systems. J. Mol. Struct. (Theochem.). 179:1988;333-352.
    • (1988) J. Mol. Struct. (Theochem.) , vol.179 , pp. 333-352
    • Li, Z.1    Scheraga, H.2
  • 26
    • 0027640931 scopus 로고
    • Genetic algorithms: Principles of natural selection applied to computation
    • Forrest S. Genetic algorithms: Principles of natural selection applied to computation. Science. 261:1993;872-878.
    • (1993) Science , vol.261 , pp. 872-878
    • Forrest, S.1
  • 27
    • 0027503403 scopus 로고
    • Reduced representation model of protein structure prediction: Stastical potential and genetic algorithms
    • Sun S. Reduced representation model of protein structure prediction: Stastical potential and genetic algorithms. Protein Sci. 2:1993;762-785.
    • (1993) Protein Sci. , vol.2 , pp. 762-785
    • Sun, S.1
  • 28
    • 34250074824 scopus 로고
    • The application of the genetic algorithm to the minimization of potential energy functions
    • LeGrand S., Merz K. The application of the genetic algorithm to the minimization of potential energy functions. J. Global Optim. 3:1993;49-66.
    • (1993) J. Global Optim. , vol.3 , pp. 49-66
    • LeGrand, S.1    Merz, K.2
  • 29
  • 31
    • 0001203963 scopus 로고
    • Global minimum potential energy conformations of small molecules
    • Maranas C., Floudas C.A. Global minimum potential energy conformations of small molecules. J. Global Optim. 4:1994;135-170.
    • (1994) J. Global Optim. , vol.4 , pp. 135-170
    • Maranas, C.1    Floudas, C.A.2
  • 32
    • 0001327501 scopus 로고
    • αBB: A global optimization method for general constrained nonconvex problems
    • Androulakis I.P., Maranas C.D., Floudas C.A. αBB: A global optimization method for general constrained nonconvex problems. J. Global. Optim. 7:1995;337-363.
    • (1995) J. Global. Optim. , vol.7 , pp. 337-363
    • Androulakis, I.P.1    Maranas, C.D.2    Floudas, C.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.