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Volumn 88, Issue 11, 2005, Pages 1759-1770

A new conformational search technique and its applications

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EID: 23644462571     PISSN: 00113891     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (14)

References (58)
  • 1
    • 0023752675 scopus 로고
    • An analysis of current methodologies for conformational searching of complex molecules
    • Howard, A. E. and Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. J. Med. Chem., 1988, 31, 1669-1675.
    • (1988) J. Med. Chem. , vol.31 , pp. 1669-1675
    • Howard, A.E.1    Kollman, P.A.2
  • 2
    • 0002015005 scopus 로고
    • A survey of methods for searching the conformational space of small and medium-sized molecules
    • (eds Lipkowitz, K. B. and Boyd, D. B.), VCH Publishers, New York
    • Leach, A. R., A survey of methods for searching the conformational space of small and medium-sized molecules. In Reviews in Computational Chemistry (eds Lipkowitz, K. B. and Boyd, D. B.), VCH Publishers, New York, 1991, vol. 2, pp. 1-55.
    • (1991) Reviews in Computational Chemistry , vol.2 , pp. 1-55
    • Leach, A.R.1
  • 3
    • 0001290941 scopus 로고
    • Conformational energy calculations on polypeptides and protein
    • Vásquez, M., Némethy, G. and Scheraga, H. A., Conformational energy calculations on polypeptides and protein. Chem. Rev., 1994, 94, 2183-2239.
    • (1994) Chem. Rev. , vol.94 , pp. 2183-2239
    • Vásquez, M.1    Némethy, G.2    Scheraga, H.A.3
  • 4
    • 0028815464 scopus 로고
    • Protein structure prediction: Recognition of primary, secondary, and tertiary structural features from amino acid sequence
    • Eisenhaber, F., Persson, B. and Argos, P., Protein structure prediction: Recognition of primary, secondary, and tertiary structural features from amino acid sequence. Crit. Rev. Biochem. Mol. Biol., 1995, 30, 1-94.
    • (1995) Crit. Rev. Biochem. Mol. Biol. , vol.30 , pp. 1-94
    • Eisenhaber, F.1    Persson, B.2    Argos, P.3
  • 5
    • 0041905968 scopus 로고    scopus 로고
    • New approaches in molecular structure prediction
    • Böhm, G., New approaches in molecular structure prediction. Biophys. Chem., 1996, 59, 1-32.
    • (1996) Biophys. Chem. , vol.59 , pp. 1-32
    • Böhm, G.1
  • 6
    • 0031236591 scopus 로고    scopus 로고
    • Molecular modeling of proteins and mathematical prediction of protein structure
    • Neumaier, A., Molecular modeling of proteins and mathematical prediction of protein structure. SIAM Rev., 1997, 39, 407-460.
    • (1997) SIAM Rev. , vol.39 , pp. 407-460
    • Neumaier, A.1
  • 8
    • 0000120464 scopus 로고    scopus 로고
    • Global optimization approaches in protein folding and peptide docking
    • (eds Farach-Colton, M. et al.), American Mathematical Society, New Jersey
    • Floudas, C. A., Klepeis, J. L. and Pardalos, P. M., Global optimization approaches in protein folding and peptide docking. In DIMACS Series in Discrete Mathematics and Theoretical Computer Science (eds Farach-Colton, M. et al.), American Mathematical Society, New Jersey, 1999, vol. 47, pp. 141-171.
    • (1999) DIMACS Series in Discrete Mathematics and Theoretical Computer Science , vol.47 , pp. 141-171
    • Floudas, C.A.1    Klepeis, J.L.2    Pardalos, P.M.3
  • 9
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner, S. J., Kollman, P. A., Nguyen, D. T. and Case, D. A., An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem., 1986, 7, 230-252.
    • (1986) J. Comput. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 11
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. 10. Improved geometrical parameters and non-bonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
    • Némethy, G. et al., Energy parameters in polypeptides. 10. Improved geometrical parameters and non-bonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem., 1992, 96, 6472-6484.
    • (1992) J. Phys. Chem. , vol.96 , pp. 6472-6484
    • Némethy, G.1
  • 12
    • 85050535270 scopus 로고
    • Optimization methods in computational chemistry
    • (eds Lipkowitz, K. B. and Boyd, D. B.), VCH Publishers, New York
    • Schlick, T., Optimization methods in computational chemistry. In Reviews in Computational Chemistry (eds Lipkowitz, K. B. and Boyd, D. B.), VCH Publishers, New York, 1992, vol. 3, pp. 1-71.
    • (1992) Reviews in Computational Chemistry , vol.3 , pp. 1-71
    • Schlick, T.1
  • 13
    • 0026776874 scopus 로고
    • Computational complexity of a problem in molecular structure prediction
    • Ngo, J. T. and Marks, J., Computational complexity of a problem in molecular structure prediction. Protein Eng., 1992, 5, 313-321.
    • (1992) Protein Eng. , vol.5 , pp. 313-321
    • Ngo, J.T.1    Marks, J.2
  • 14
    • 0023173201 scopus 로고
    • Prediction of the folding of short polypeptide segments by uniform conformational sampling
    • Bruccoleri, R. E. and Karplus, M., Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers, 1987, 26, 137-168.
    • (1987) Biopolymers , vol.26 , pp. 137-168
    • Bruccoleri, R.E.1    Karplus, M.2
  • 15
    • 84988099596 scopus 로고
    • Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization
    • Gibson, K. D. and Scheraga, H. A., Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization. J. Comput. Chem., 1987, 8, 826-834.
    • (1987) J. Comput. Chem. , vol.8 , pp. 826-834
    • Gibson, K.D.1    Scheraga, H.A.2
  • 16
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li, Z. and Scheraga, H. A., Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. USA, 1987, 84, 6611-6615.
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 17
    • 0024604167 scopus 로고
    • The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: Tests on enkephalin
    • Ripoll, D. R. and Scheraga, H. A., The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: Tests on enkephalin. J. Protein Chem., 1989, 8, 263-287.
    • (1989) J. Protein Chem. , vol.8 , pp. 263-287
    • Ripoll, D.R.1    Scheraga, H.A.2
  • 18
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, S., Gelatt, C. D. and Vecchi, M. P., Optimization by simulated annealing. Science, 1983, 220, 671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 19
    • 0025164892 scopus 로고
    • Applications of simulated annealing to peptides
    • Wilson, S. R. and Cui, W. L., Applications of simulated annealing to peptides. Biopolymers, 1990, 29, 225-235.
    • (1990) Biopolymers , vol.29 , pp. 225-235
    • Wilson, S.R.1    Cui, W.L.2
  • 20
    • 0026065046 scopus 로고
    • Applications of simulated annealing to the multiple-minima problem in small peptides
    • Morales, L. B., Garduno-Juárez, R. and Romero, D., Applications of simulated annealing to the multiple-minima problem in small peptides. J. Biomol. Struct. Dyn., 1991, 8, 721-735.
    • (1991) J. Biomol. Struct. Dyn. , vol.8 , pp. 721-735
    • Morales, L.B.1    Garduno-Juárez, R.2    Romero, D.3
  • 21
    • 0003682904 scopus 로고
    • The genetic algorithm and protein structure prediction
    • (eds Merz, K. M. and Le Grand, S. M.), Birkhäuser, Boston
    • Le Grand, S. M. and Merz, K. M., The genetic algorithm and protein structure prediction. In The Protein Folding Problem and Tertiary Structure Prediction (eds Merz, K. M. and Le Grand, S. M.), Birkhäuser, Boston, 1994, pp. 109-124.
    • (1994) The Protein Folding Problem and Tertiary Structure Prediction , pp. 109-124
    • Le Grand, S.M.1    Merz, K.M.2
  • 22
    • 0034572961 scopus 로고    scopus 로고
    • Genetic algorithm and protein folding
    • (ed. Webster, D. M.), Humana Press, New Jersey
    • Schulze-Kremer, S., Genetic algorithm and protein folding. In Protein Structure Prediction - Methods and Protocols (ed. Webster, D. M.), Humana Press, New Jersey, 2000, pp. 175-222.
    • (2000) Protein Structure Prediction - Methods and Protocols , pp. 175-222
    • Schulze-Kremer, S.1
  • 23
    • 0003068337 scopus 로고
    • Building protein folds using distance geometry: Towards a general modeling and prediction method
    • (eds Merz, K. M. and Le Grand, S. M.), Birkhäuser, Boston
    • Taylor, W. R. and Aszódi, A., Building protein folds using distance geometry: Towards a general modeling and prediction method. In The Protein Folding Problem and Tertiary Structure Prediction (eds Merz, K. M. and Le Grand, S. M.), Birkhäuser, Boston, 1994, pp. 165-192.
    • (1994) The Protein Folding Problem and Tertiary Structure Prediction , pp. 165-192
    • Taylor, W.R.1    Aszódi, A.2
  • 24
    • 0000594925 scopus 로고
    • The multiple-minima problem in the conformational analysis of molecules: Deformation of potential energy hyper surface by diffusion equation method
    • Piela, L., Kostrowicki, J. and Scheraga, H. A., The multiple-minima problem in the conformational analysis of molecules: Deformation of potential energy hyper surface by diffusion equation method. J. Phys. Chem., 1989, 93, 3339-3346.
    • (1989) J. Phys. Chem. , vol.93 , pp. 3339-3346
    • Piela, L.1    Kostrowicki, J.2    Scheraga, H.A.3
  • 25
    • 0001031118 scopus 로고
    • Application of diffusion equation method for global optimization to oligopeptides
    • Kostrowicki, J. and Scheraga, H. A., Application of diffusion equation method for global optimization to oligopeptides. J. Phys. Chem., 1992, 96, 7442-7449.
    • (1992) J. Phys. Chem. , vol.96 , pp. 7442-7449
    • Kostrowicki, J.1    Scheraga, H.A.2
  • 26
    • 84986483796 scopus 로고
    • Variable step molecular dynamics: An exploratory technique for peptides with fixed geometry
    • Gibson, K. D. and Scheraga, H. A., Variable step molecular dynamics: An exploratory technique for peptides with fixed geometry. J. Comput. Chem., 1990, 11, 468-486.
    • (1990) J. Comput. Chem. , vol.11 , pp. 468-486
    • Gibson, K.D.1    Scheraga, H.A.2
  • 27
    • 0007793280 scopus 로고
    • Conformations of cycloheptadecane. a comparison of methods for conformational searching
    • Saunders, M., Houk, K. N., Wu, Y. D., Still, W. C., Lipton, M., Chang, G. and Guida, W. C., Conformations of cycloheptadecane. A comparison of methods for conformational searching. J. Am. Chem. Soc., 1990, 112, 1419-1427.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 1419-1427
    • Saunders, M.1    Houk, K.N.2    Wu, Y.D.3    Still, W.C.4    Lipton, M.5    Chang, G.6    Guida, W.C.7
  • 28
    • 0037305932 scopus 로고    scopus 로고
    • Hybrid global optimization algorithms for protein structure prediction: Alternating hybrids
    • Klepeis, J. L., Pieja, M. J. and Floudas, C. A., Hybrid global optimization algorithms for protein structure prediction: Alternating hybrids. Biophys. J., 2003, 84, 869-882.
    • (2003) Biophys. J. , vol.84 , pp. 869-882
    • Klepeis, J.L.1    Pieja, M.J.2    Floudas, C.A.3
  • 29
    • 0038298788 scopus 로고    scopus 로고
    • Enhanced sampling of the molecular potential energy surface using mutually orthogonal Latin squares: Application to peptide structures
    • Vengadesan, K. and Gautham, N., Enhanced sampling of the molecular potential energy surface using mutually orthogonal Latin squares: Application to peptide structures. Biophys. J., 2003, 84, 2897-2906.
    • (2003) Biophys. J. , vol.84 , pp. 2897-2906
    • Vengadesan, K.1    Gautham, N.2
  • 30
    • 33645178206 scopus 로고
    • Randomized blocks and Latin squares
    • Cambridge University Press, London
    • Finney, D. J., Randomized blocks and Latin squares. In Experimental Design and its Statistical Basis, Cambridge University Press, London, 1955, pp. 45-67.
    • (1955) Experimental Design and Its Statistical Basis , pp. 45-67
    • Finney, D.J.1
  • 31
    • 33645173739 scopus 로고
    • The Latin square
    • Oliver and Boyd, London, 7th edn
    • Fisher, R. A., The Latin square. In The Design of Experiments, Oliver and Boyd, London, 1960, 7th edn, pp. 70-92.
    • (1960) The Design of Experiments , pp. 70-92
    • Fisher, R.A.1
  • 32
    • 0040988516 scopus 로고    scopus 로고
    • Randomized blocks, Latin squares, and related designs
    • John Wiley, New York, 5th edn
    • Montgomery, D. C., Randomized blocks, Latin squares, and related designs. In Design and Analysis of Experiments, John Wiley, New York, 2000, 5th edn, pp. 126-169.
    • (2000) Design and Analysis of Experiments , pp. 126-169
    • Montgomery, D.C.1
  • 33
    • 0037598928 scopus 로고
    • Global search for optimal biomolecular structures using mutually orthogonal Latin squares
    • Gautham, N. and Rafi, Z. A., Global search for optimal biomolecular structures using mutually orthogonal Latin squares. Curr. Sci., 1992, 63, 560-564.
    • (1992) Curr. Sci. , vol.63 , pp. 560-564
    • Gautham, N.1    Rafi, Z.A.2
  • 35
    • 0034829669 scopus 로고    scopus 로고
    • Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-α-aminoisobutyric acid in vacuo
    • Improta, R., Barone, V., Kudin, K. N. and Scuseria, G. E., Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-α-aminoisobutyric acid in vacuo. J. Am. Chem. Soc., 2001, 123, 3311-3322.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 3311-3322
    • Improta, R.1    Barone, V.2    Kudin, K.N.3    Scuseria, G.E.4
  • 36
    • 0013815214 scopus 로고
    • Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units
    • Ramakrishnan, C. and Ramachandran, G. N., Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. Biophys. J., 1965, 5, 909-933.
    • (1965) Biophys. J. , vol.5 , pp. 909-933
    • Ramakrishnan, C.1    Ramachandran, G.N.2
  • 37
    • 0014347799 scopus 로고
    • Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units
    • Venkatachalam, C. M., Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers, 1968, 6, 1425-1436.
    • (1968) Biopolymers , vol.6 , pp. 1425-1436
    • Venkatachalam, C.M.1
  • 42
    • 0015767632 scopus 로고
    • An obligatory α-helical amino acid residue
    • Burgess, A. W. and Leach, S. J., An obligatory α-helical amino acid residue. Biopolymers, 1973, 12, 2599-2605.
    • (1973) Biopolymers , vol.12 , pp. 2599-2605
    • Burgess, A.W.1    Leach, S.J.2
  • 43
    • 0035128033 scopus 로고    scopus 로고
    • Energy landscapes of conformationally constrained peptides
    • Levy, Y. and Becker, O. M., Energy landscapes of conformationally constrained peptides. J. Chem. Phys., 2001, 14, 993-1009.
    • (2001) J. Chem. Phys. , vol.14 , pp. 993-1009
    • Levy, Y.1    Becker, O.M.2
  • 44
    • 4344627663 scopus 로고    scopus 로고
    • Conformational studies on enkephalins using the MOLS technique
    • Vengadesan, K. and Gautham, N., Conformational studies on enkephalins using the MOLS technique. Biopolymers, 2004, 74, 476-494.
    • (2004) Biopolymers , vol.74 , pp. 476-494
    • Vengadesan, K.1    Gautham, N.2
  • 45
    • 0000447708 scopus 로고
    • Conformational analysis of enkephalin and conformation-activity relationships
    • (eds Udenfriend, S. and Meienhofer, J.), Academic Press, New York
    • Schiller, P. W., Conformational analysis of enkephalin and conformation-activity relationships. In The Peptides: Analysis, Synthesis, Biology (eds Udenfriend, S. and Meienhofer, J.), Academic Press, New York, 1984, vol. 6, pp. 219-268.
    • (1984) The Peptides: Analysis, Synthesis, Biology , vol.6 , pp. 219-268
    • Schiller, P.W.1
  • 46
    • 0029671001 scopus 로고    scopus 로고
    • Structural studies of opioid peptides: A review of recent progress in X-ray diffraction studies
    • Deschamps, J. R., George, C. and Flippen-Anderson, J. L., Structural studies of opioid peptides: A review of recent progress in X-ray diffraction studies. Biopolymers, 1996, 40, 121-139.
    • (1996) Biopolymers , vol.40 , pp. 121-139
    • Deschamps, J.R.1    George, C.2    Flippen-Anderson, J.L.3
  • 47
    • 0030972502 scopus 로고    scopus 로고
    • Molecular dynamics simulations of Leu-enkephalin in water and DMSO
    • van der Spoel, D. and Berendsen, H. J. C., Molecular dynamics simulations of Leu-enkephalin in water and DMSO. Biophys. J., 1997, 72, 2032-2041.
    • (1997) Biophys. J. , vol.72 , pp. 2032-2041
    • Van Der Spoel, D.1    Berendsen, H.J.C.2
  • 49
    • 4043131647 scopus 로고    scopus 로고
    • The energy landscape of Met-enkephalin and Leu-enkephalin drawn using mutually orthogonal Latin squares sampling
    • Vengadesan, K. and Gautham, N., The energy landscape of Met-enkephalin and Leu-enkephalin drawn using mutually orthogonal Latin squares sampling. J. Phys. Chem. B, 2004, 108, 11196-11205.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 11196-11205
    • Vengadesan, K.1    Gautham, N.2
  • 50
    • 0037621436 scopus 로고    scopus 로고
    • Energy levels and quantum states of [Leu]enkephalin conformations based on theoretical and experimental investigations
    • Abdali, S., Jensen, M. Ø. and Bohr, H., Energy levels and quantum states of [Leu]enkephalin conformations based on theoretical and experimental investigations. J. Phys. Condens. Matter, 2003, 15, S1853-S1860.
    • (2003) J. Phys. Condens. Matter , vol.15
    • Abdali, S.1    Jensen, M.Ø.2    Bohr, H.3
  • 51
    • 1642312808 scopus 로고    scopus 로고
    • An application of experimental design using mutually orthogonal Latin squares in conformational studies of peptides
    • Vengadesan, K., Anbupalam, T. and Gautham, N., An application of experimental design using mutually orthogonal Latin squares in conformational studies of peptides. Biochem. Biophys. Res. Commun., 2004, 316, 731-737.
    • (2004) Biochem. Biophys. Res. Commun. , vol.316 , pp. 731-737
    • Vengadesan, K.1    Anbupalam, T.2    Gautham, N.3
  • 52
    • 0034625279 scopus 로고    scopus 로고
    • Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals
    • Lee, J. et al., Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals. Comput. Phys. Commun., 2000, 128, 399-411.
    • (2000) Comput. Phys. Commun. , vol.128 , pp. 399-411
    • Lee, J.1
  • 56
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • Rost, B. and Sander, C. J., Prediction of protein secondary structure at better than 70% accuracy. Mol. Biol., 1993, 232, 584-599.
    • (1993) Mol. Biol. , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.J.2
  • 57
    • 0034480326 scopus 로고    scopus 로고
    • NMR strucutres of biomolecules using field oriented media and residual dipolar couplings
    • Prestegard, J. H., Al-Hashimi, H. M. and Tolman, J. R., NMR strucutres of biomolecules using field oriented media and residual dipolar couplings. Q. Rev. Biophys., 2000, 33, 371-424.
    • (2000) Q. Rev. Biophys. , vol.33 , pp. 371-424
    • Prestegard, J.H.1    Al-Hashimi, H.M.2    Tolman, J.R.3
  • 58
    • 0037936914 scopus 로고
    • Latin squares
    • MIT Press, Cambridge, Massachusetts
    • Ito, K., Latin squares. In Encyclopedic Dictionary of Mathematics, MIT Press, Cambridge, Massachusetts, 1987, vol. 2, pp. 891-892.
    • (1987) Encyclopedic Dictionary of Mathematics , vol.2 , pp. 891-892
    • Ito, K.1


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