메뉴 건너뛰기




Volumn 15, Issue 3, 1999, Pages 235-260

Surmounting the Multiple-Minima Problem in Protein Folding

Author keywords

Global optimization; Multiple minima problem; Protein folding; Structure prediction

Indexed keywords


EID: 0004416927     PISSN: 09255001     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008328218931     Document Type: Article
Times cited : (29)

References (81)
  • 1
    • 0033610078 scopus 로고    scopus 로고
    • Global optimization of clusters, crystals and biomolecules
    • Wales, D.J. and Scheraga, H.A. (1999), Global optimization of clusters, crystals and biomolecules, Science, 285: 1368-1372.
    • (1999) Science , vol.285 , pp. 1368-1372
    • Wales, D.J.1    Scheraga, H.A.2
  • 2
    • 5944250450 scopus 로고
    • Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions and intrinsic torsional potential for the naturally occurring aminoacids
    • Momany, F.A., McGuire, R.F., Burgess, A.W. and Scheraga, H.A. (1975), Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions and intrinsic torsional potential for the naturally occurring aminoacids, J. Phys. Chem. 79: 2361-2381.
    • (1975) J. Phys. Chem. , vol.79 , pp. 2361-2381
    • Momany, F.A.1    McGuire, R.F.2    Burgess, A.W.3    Scheraga, H.A.4
  • 3
    • 33845550595 scopus 로고
    • Energy parameters in polypeptides. IX. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids
    • Némethy, G., Pottle, M.S. and Scheraga, H.A. (1983), Energy parameters in polypeptides. IX. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids, J. Phys. Chem. 87: 1883-1887.
    • (1983) J. Phys. Chem. , vol.87 , pp. 1883-1887
    • Némethy, G.1    Pottle, M.S.2    Scheraga, H.A.3
  • 4
    • 27244454740 scopus 로고
    • Intermolecular potentials from crystal data. VI. Determination of empirical potentials for O-H⋯O-C hydrogen bonds from packing configurations
    • Sippl, M.J., Némethy, G. and Scheraga, H.A. (1984), Intermolecular potentials from crystal data. VI. Determination of empirical potentials for O-H⋯O-C hydrogen bonds from packing configurations, J. Phys. Chem. 88: 6231-6233.
    • (1984) J. Phys. Chem. , vol.88 , pp. 6231-6233
    • Sippl, M.J.1    Némethy, G.2    Scheraga, H.A.3
  • 5
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. X. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
    • Némethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S. and Scheraga, H.A. (1992), Energy parameters in polypeptides. X. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides, J. Phys. Chem. 96: 6472-6484.
    • (1992) J. Phys. Chem. , vol.96 , pp. 6472-6484
    • Némethy, G.1    Gibson, K.D.2    Palmer, K.A.3    Yoon, C.N.4    Paterlini, G.5    Zagari, A.6    Rumsey, S.7    Scheraga, H.A.8
  • 6
    • 0027524668 scopus 로고
    • Calculation of protein backbone geometry from α-carbon coordinates based on peptide-group dipole alignment
    • Liwo, A., Pincus, M.R., Wawak, R.J., Rackovsky, S. and Scheraga, H.A. (1993), Calculation of protein backbone geometry from α-carbon coordinates based on peptide-group dipole alignment, Protein Science 2: 1697-1714.
    • (1993) Protein Science , vol.2 , pp. 1697-1714
    • Liwo, A.1    Pincus, M.R.2    Wawak, R.J.3    Rackovsky, S.4    Scheraga, H.A.5
  • 7
    • 0027435091 scopus 로고
    • Prediction of protein conformation on the basis of a search for compact structures; test on avian pancreatic polypeptide
    • Liwo, A., Pincus, M.R., Wawak, R.J., Rackovsky, S. and Scheraga, H.A. (1993), Prediction of protein conformation on the basis of a search for compact structures; test on avian pancreatic polypeptide, Protein Science 2: 1715-1731.
    • (1993) Protein Science , vol.2 , pp. 1715-1731
    • Liwo, A.1    Pincus, M.R.2    Wawak, R.J.3    Rackovsky, S.4    Scheraga, H.A.5
  • 8
    • 0000095892 scopus 로고    scopus 로고
    • A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data
    • Liwo, A., Oldziej, S., Pincus, M.R., Wawak, R.J., Rackovsky, S. and Scheraga, H.A. (1997), A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data, J. Comput. Chem. 18: 849-873.
    • (1997) J. Comput. Chem. , vol.18 , pp. 849-873
    • Liwo, A.1    Oldziej, S.2    Pincus, M.R.3    Wawak, R.J.4    Rackovsky, S.5    Scheraga, H.A.6
  • 9
    • 0000095890 scopus 로고    scopus 로고
    • A united-residue force field for off-lattice protein-structure simulations. II: Parameterization of short-range interactions and determination of the weights of energy terms by Z-score optimization
    • Liwo, A., Pincus, M.R., Wawak, R.J., Rackovsky, S., Oldziej, S. and Scheraga, H.A. (1997), A united-residue force field for off-lattice protein-structure simulations. II: Parameterization of short-range interactions and determination of the weights of energy terms by Z-score optimization, J. Comput. Chem. 18: 874-887.
    • (1997) J. Comput. Chem. , vol.18 , pp. 874-887
    • Liwo, A.1    Pincus, M.R.2    Wawak, R.J.3    Rackovsky, S.4    Oldziej, S.5    Scheraga, H.A.6
  • 10
    • 0001181898 scopus 로고    scopus 로고
    • A united-residue force field for off-lattice protein-structure simulations. III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials
    • Liwo, A., Kazmierkiewicz, R., Czaplewski, C., Groth, M., Oldziej, S., Wawak, R.J., Rackovsky, S., Pincus, M.R. and Scheraga, H.A. (1998), A united-residue force field for off-lattice protein-structure simulations. III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials, J. Comput. Chem. 19: 259-276.
    • (1998) J. Comput. Chem. , vol.19 , pp. 259-276
    • Liwo, A.1    Kazmierkiewicz, R.2    Czaplewski, C.3    Groth, M.4    Oldziej, S.5    Wawak, R.J.6    Rackovsky, S.7    Pincus, M.R.8    Scheraga, H.A.9
  • 11
    • 0347525711 scopus 로고
    • Prediction of protein conformation
    • C.B. Anfinsen and A.N. Schechter (eds.), Academic Press, New York
    • Scheraga, H.A. (1974), Prediction of protein conformation, in C.B. Anfinsen and A.N. Schechter (eds.), Current Topics in Biochemistry (pp. 1-42), Academic Press, New York.
    • (1974) Current Topics in Biochemistry , pp. 1-42
    • Scheraga, H.A.1
  • 12
    • 0042153813 scopus 로고
    • Conformational energy calculations of the effects of sequence variations on the conformations of two tetrapeptides
    • Simon, I., Némethy, G. and Scheraga, H.A. (1978), Conformational energy calculations of the effects of sequence variations on the conformations of two tetrapeptides, Macromolecules 11: 797-804.
    • (1978) Macromolecules , vol.11 , pp. 797-804
    • Simon, I.1    Némethy, G.2    Scheraga, H.A.3
  • 13
    • 0020170122 scopus 로고
    • Calculation of the three-dimensional structure of the membrane-bound portion of melittin from its amino acid sequence
    • Pincus, M.R., Klausner, R.D. and Scheraga, H.A. (1982), Calculation of the three-dimensional structure of the membrane-bound portion of melittin from its amino acid sequence, Proc. Natl. Acad. Sci., USA 79: 5107-5110.
    • (1982) Proc. Natl. Acad. Sci., USA , vol.79 , pp. 5107-5110
    • Pincus, M.R.1    Klausner, R.D.2    Scheraga, H.A.3
  • 14
    • 0020648227 scopus 로고
    • Recent progress in the theoretical treatment of protein folding
    • Scheraga, H.A. (1983), Recent progress in the theoretical treatment of protein folding, Biopolymers 22: 1-14.
    • (1983) Biopolymers , vol.22 , pp. 1-14
    • Scheraga, H.A.1
  • 15
    • 0021813809 scopus 로고
    • Use of buildup and energy-minimization procedures to compute low-energy structures of the backbone of enkephalin
    • Vásquez, M. and Scheraga, H.A. (1985), Use of buildup and energy-minimization procedures to compute low-energy structures of the backbone of enkephalin, Biopolymers 24: 1437-1447.
    • (1985) Biopolymers , vol.24 , pp. 1437-1447
    • Vásquez, M.1    Scheraga, H.A.2
  • 16
    • 84988099596 scopus 로고
    • Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization
    • Gibson, K.D. and Scheraga, H.A. (1987), Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization, J. Comput. Chem. 8: 826-834.
    • (1987) J. Comput. Chem. , vol.8 , pp. 826-834
    • Gibson, K.D.1    Scheraga, H.A.2
  • 17
    • 0001298333 scopus 로고
    • Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue α-aminobutyric acid
    • Vásquez, M., Némethy, G. and Scheraga, H.A. (1983), Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue α-aminobutyric acid, Macromolecules 16: 1043-1049.
    • (1983) Macromolecules , vol.16 , pp. 1043-1049
    • Vásquez, M.1    Némethy, G.2    Scheraga, H.A.3
  • 18
    • 0017435119 scopus 로고
    • Conformational analysis of the twenty naturally occurring amino acid residues using ECEPP
    • Zimmerman, S.S., Pottle, M.S., Némethy, G. and Scheraga, H.A. (1977), Conformational analysis of the twenty naturally occurring amino acid residues using ECEPP, Macromolecules 10: 1-9.
    • (1977) Macromolecules , vol.10 , pp. 1-9
    • Zimmerman, S.S.1    Pottle, M.S.2    Némethy, G.3    Scheraga, H.A.4
  • 19
    • 0023921186 scopus 로고
    • Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data
    • Vásquez, M. and Scheraga, H.A. (1988), Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data, J. Biomol. Struct. & Dyn. 5: 705-755.
    • (1988) J. Biomol. Struct. & Dyn. , vol.5 , pp. 705-755
    • Vásquez, M.1    Scheraga, H.A.2
  • 20
    • 0023914645 scopus 로고
    • Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data
    • Vásquez, M. and Scheraga, H.A. (1988), Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data, J. Biomol. Struct. & Dyn. 5: 757-784.
    • (1988) J. Biomol. Struct. & Dyn. , vol.5 , pp. 757-784
    • Vásquez, M.1    Scheraga, H.A.2
  • 21
    • 0016579644 scopus 로고
    • Use of a symmetry condition to compute the conformation of gramicidin S
    • Dygert, M., Gō, N. and Scheraga, H.A. (1975), Use of a symmetry condition to compute the conformation of gramicidin S, Macromolecules 8: 750-761.
    • (1975) Macromolecules , vol.8 , pp. 750-761
    • Dygert, M.1    Go, N.2    Scheraga, H.A.3
  • 22
    • 0021343559 scopus 로고
    • Hydrogen bonding involving the ornithine side chain of gramicidin S
    • Némethy, G. and Scheraga, H.A. (1984), Hydrogen bonding involving the ornithine side chain of gramicidin S, Biochem. Biophys. Res. Commun. 118: 643-647.
    • (1984) Biochem. Biophys. Res. Commun. , vol.118 , pp. 643-647
    • Némethy, G.1    Scheraga, H.A.2
  • 23
    • 0000925139 scopus 로고
    • Calculation of the structures of collagen models. Role of interchain interactions in determining the triple-helical coiled-coil conformation. 1. Poly(glycyl-prolyl-prolyl)
    • Miller, M.H. and Scheraga, H.A. (1976), Calculation of the structures of collagen models. Role of interchain interactions in determining the triple-helical coiled-coil conformation. 1. Poly(glycyl-prolyl-prolyl), J. Polymer Sci.: Polymer Symposia No. 54, pp. 171-200.
    • (1976) J. Polymer Sci.: Polymer Symposia No. 54 , pp. 171-200
    • Miller, M.H.1    Scheraga, H.A.2
  • 24
    • 0000121283 scopus 로고
    • Calculation of the structures of collagen models. Role of interchain interactions in determining the triple-helical coiled-coil conformation. 2. Poly(glycyl-prolyl-hydroxyprolyl)
    • Miller, M.H., Némethy, G. and Scheraga, H.A. (1980), Calculation of the structures of collagen models. Role of interchain interactions in determining the triple-helical coiled-coil conformation. 2. Poly(glycyl-prolyl-hydroxyprolyl), Macromolecules 13: 470-478.
    • (1980) Macromolecules , vol.13 , pp. 470-478
    • Miller, M.H.1    Némethy, G.2    Scheraga, H.A.3
  • 25
    • 0011767776 scopus 로고
    • Calculation of the structures of collagen models. Role of interchain interactions in determining the triple-helical coiled-coil conformation. 3. Poly(glycyl-prolyl-alanyl)
    • Miller, M.H., Némethy, G. and Scheraga, H.A. (1980), Calculation of the structures of collagen models. Role of interchain interactions in determining the triple-helical coiled-coil conformation. 3. Poly(glycyl-prolyl-alanyl), Macromolecules 13: 910-913.
    • (1980) Macromolecules , vol.13 , pp. 910-913
    • Miller, M.H.1    Némethy, G.2    Scheraga, H.A.3
  • 26
    • 0017309766 scopus 로고
    • Structural patterns in globular proteins
    • Levitt, M. and Chothia, C. (1976), Structural patterns in globular proteins, Nature 261: 552-558.
    • (1976) Nature , vol.261 , pp. 552-558
    • Levitt, M.1    Chothia, C.2
  • 27
    • 0017292056 scopus 로고
    • The α-helix as an electric macro-dipole
    • Wada, A. (1976), The α-helix as an electric macro-dipole, Adv. Biophys. 9: 1-63.
    • (1976) Adv. Biophys. , vol.9 , pp. 1-63
    • Wada, A.1
  • 28
    • 0018094892 scopus 로고
    • Electrostatic effects in proteins
    • Perutz, M.F. (1978), Electrostatic effects in proteins, Science 201: 1187-1191.
    • (1978) Science , vol.201 , pp. 1187-1191
    • Perutz, M.F.1
  • 29
    • 0019776488 scopus 로고
    • Dipoles of the α-helix and β-sheet: Their role in protein folding
    • Hol, W.G.J., Halie, L.M. and Sander, C. (1981), Dipoles of the α-helix and β-sheet: their role in protein folding, Nature 294: 532-536.
    • (1981) Nature , vol.294 , pp. 532-536
    • Hol, W.G.J.1    Halie, L.M.2    Sander, C.3
  • 30
    • 33748308467 scopus 로고
    • Energetic approach to the packing of α-helices. 1. Equivalent helices
    • Chou, K.-C., Némethy, G. and Scheraga, H.A. (1983), Energetic approach to the packing of α-helices. 1. Equivalent helices, J. Phys. Chem. 87: 2869-2881.
    • (1983) J. Phys. Chem. , vol.87 , pp. 2869-2881
    • Chou, K.-C.1    Némethy, G.2    Scheraga, H.A.3
  • 31
    • 0021978310 scopus 로고
    • The role of the α-helix dipole in protein function and structure
    • Hol, W.G.J. (1985), The role of the α-helix dipole in protein function and structure, Prog. Biophys. molec. Biol. 45: 149-195.
    • (1985) Prog. Biophys. Molec. Biol. , vol.45 , pp. 149-195
    • Hol, W.G.J.1
  • 32
    • 0002164256 scopus 로고
    • On the multiple-minima problem in the conformational analysis of polypeptides. I. Backbone degrees of freedom for a perturbed α-helix
    • Piela, L. and Scheraga, H.A. (1987), On the multiple-minima problem in the conformational analysis of polypeptides. I. Backbone degrees of freedom for a perturbed α-helix, Biopolymers 26: S33-S58.
    • (1987) Biopolymers , vol.26
    • Piela, L.1    Scheraga, H.A.2
  • 33
    • 0026005891 scopus 로고
    • On the multiple-minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven Monte Carlo methods to bovine pancreatic trypsin inhibitor
    • Ripoll, D.R., Piela, L., Vásquez, M. and Scheraga, H.A. (1991), On the multiple-minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven Monte Carlo methods to bovine pancreatic trypsin inhibitor, Proteins: Struc., Func., and Gen. 10: 188-198.
    • (1991) Proteins: Struc., Func., and Gen. , vol.10 , pp. 188-198
    • Ripoll, D.R.1    Piela, L.2    Vásquez, M.3    Scheraga, H.A.4
  • 34
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li, Z. and Scheraga, H.A. (1987), Monte Carlo-minimization approach to the multiple-minima problem in protein folding, Proc. Natl. Acad. Sci., USA 84: 6611-6615.
    • (1987) Proc. Natl. Acad. Sci., USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 35
    • 0001643360 scopus 로고
    • Structure and free energy of complex thermodynamic systems
    • Li, Z. and Scheraga, H.A. (1988), Structure and free energy of complex thermodynamic systems, J. Molec. Str. (Theochem) 179: 333-352.
    • (1988) J. Molec. Str. (Theochem) , vol.179 , pp. 333-352
    • Li, Z.1    Scheraga, H.A.2
  • 38
    • 0001182617 scopus 로고
    • Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results
    • Hagler, A.T., Stern, P.S., Sharon, R., Becker, J.M. and Naider, F. (1979), Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results, J. Am. Chem. Soc. 101: 6842-6852.
    • (1979) J. Am. Chem. Soc. , vol.101 , pp. 6842-6852
    • Hagler, A.T.1    Stern, P.S.2    Sharon, R.3    Becker, J.M.4    Naider, F.5
  • 39
    • 0010467337 scopus 로고
    • Evolution and stability of polypeptide chain conformation: A simulation study
    • Rapaport, D.C. and Scheraga, H.A. (1981), Evolution and stability of polypeptide chain conformation: a simulation study, Macromolecules 14: 1238-1246.
    • (1981) Macromolecules , vol.14 , pp. 1238-1246
    • Rapaport, D.C.1    Scheraga, H.A.2
  • 40
    • 0022105875 scopus 로고
    • Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin
    • Paine, G.H. and Scheraga, H.A. (1985), Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin, Biopolymers 24: 1391-1436.
    • (1985) Biopolymers , vol.24 , pp. 1391-1436
    • Paine, G.H.1    Scheraga, H.A.2
  • 41
    • 0020949717 scopus 로고
    • Algorithm 611. Subroutines for unconstrained minimization using a model/trust-region approach
    • Gay, D.M. (1983), Algorithm 611. Subroutines for unconstrained minimization using a model/trust-region approach, ACM Trans. Math. Software 9: 503-524.
    • (1983) ACM Trans. Math. Software , vol.9 , pp. 503-524
    • Gay, D.M.1
  • 42
    • 0024066560 scopus 로고
    • On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method-tests on poly(L-alanine)
    • Ripoll, D.R. and Scheraga, H.A. (1988), On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method-tests on poly(L-alanine), Biopolymers 27: 1283-1303.
    • (1988) Biopolymers , vol.27 , pp. 1283-1303
    • Ripoll, D.R.1    Scheraga, H.A.2
  • 43
    • 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. (1989), The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method; tests on enkephalin, J. Protein Chem. 8: 263-287.
    • (1989) J. Protein Chem. , vol.8 , pp. 263-287
    • Ripoll, D.R.1    Scheraga, H.A.2
  • 44
    • 0032146488 scopus 로고    scopus 로고
    • New developments of the electrostatically driven Monte Carlo method - Test on the membrane bound portion of melittin
    • Ripoll, D.R., Liwo, A. and Scheraga, H.A. (1998), New developments of the electrostatically driven Monte Carlo method - Test on the membrane bound portion of melittin, Biopolymers 46: 117-126.
    • (1998) Biopolymers , vol.46 , pp. 117-126
    • Ripoll, D.R.1    Liwo, A.2    Scheraga, H.A.3
  • 46
    • 0026103603 scopus 로고
    • The electrostatically driven Monte Carlo method: Application to conformational analysis of decaglycine
    • Ripoll, D.R., Vásquez, M.J. and Scheraga, H.A. (1991), The electrostatically driven Monte Carlo method: Application to conformational analysis of decaglycine, Biopolymers 31: 319-330.
    • (1991) Biopolymers , vol.31 , pp. 319-330
    • Ripoll, D.R.1    Vásquez, M.J.2    Scheraga, H.A.3
  • 47
    • 0026619157 scopus 로고
    • Conformational study of a peptide epitope shows large preferences for β-turn conformations
    • Ripoll, D.R. (1992), Conformational study of a peptide epitope shows large preferences for β-turn conformations, Int. J. Pepide Protein Res. 40: 575-581.
    • (1992) Int. J. Pepide Protein Res. , vol.40 , pp. 575-581
    • Ripoll, D.R.1
  • 48
    • 0026571369 scopus 로고
    • Conformational analysis of a twelve-residue analogue of mastoparan and mastoparan X
    • Faerman, C.H. and Ripoll, D.R. (1992), Conformational analysis of a twelve-residue analogue of mastoparan and mastoparan X, Proteins 12: 111-116.
    • (1992) Proteins , vol.12 , pp. 111-116
    • Faerman, C.H.1    Ripoll, D.R.2
  • 49
    • 0028207563 scopus 로고
    • Comparison of the low energy conformations of an oncogenic and a non-oncogenic p21 protein, neither of which binds GTP or GDP
    • Liwo, A., Gibson, K.D., Scheraga, H.A., Brandt-Rauf, P.W., Monaco, R. and Pincus, M.R. (1994), Comparison of the low energy conformations of an oncogenic and a non-oncogenic p21 protein, neither of which binds GTP or GDP, J. Protein Chem. 13: 237-251.
    • (1994) J. Protein Chem. , vol.13 , pp. 237-251
    • Liwo, A.1    Gibson, K.D.2    Scheraga, H.A.3    Brandt-Rauf, P.W.4    Monaco, R.5    Pincus, M.R.6
  • 51
    • 0030582736 scopus 로고    scopus 로고
    • Coupling between folding and ionization equilibria. Effects of pH on the conformational preferences of polypeptides
    • Ripoll, D.R., Vorobjev, Y.N., Liwo, A., Vila, J.A. and Scheraga, H.A. (1996), Coupling between folding and ionization equilibria. Effects of pH on the conformational preferences of polypeptides, J. Mol. Biol. 264: 770-783.
    • (1996) J. Mol. Biol. , vol.264 , pp. 770-783
    • Ripoll, D.R.1    Vorobjev, Y.N.2    Liwo, A.3    Vila, J.A.4    Scheraga, H.A.5
  • 52
    • 0031768734 scopus 로고    scopus 로고
    • Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing α-helices
    • Vila, J.A., Ripoll, D.R., Villegas, M.E., Vorobjev, Y.N. and Scheraga, H.A. (1998), Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing α-helices, Biophys. J. 75: 2637-2646.
    • (1998) Biophys. J. , vol.75 , pp. 2637-2646
    • Vila, J.A.1    Ripoll, D.R.2    Villegas, M.E.3    Vorobjev, Y.N.4    Scheraga, H.A.5
  • 54
    • 0000911717 scopus 로고
    • Mean-field theory as a tool for intramolecular conformational optimization. 1. Tests on terminally-blocked alanine and Metenkephalin
    • Olszewski, K.A., Piela, L. and Scheraga, H.A. (1992), Mean-field theory as a tool for intramolecular conformational optimization. 1. Tests on terminally-blocked alanine and Metenkephalin, J. Phys. Chem. 96: 4672-4676.
    • (1992) J. Phys. Chem. , vol.96 , pp. 4672-4676
    • Olszewski, K.A.1    Piela, L.2    Scheraga, H.A.3
  • 55
    • 0040976839 scopus 로고
    • Mean field theory as a tool for intramolecular conformational optimization. 2. Tests on the homopolypeptides decaglycine and icosalanine
    • Olszewski, K.A., Piela, L. and Scheraga, H.A. (1993), Mean field theory as a tool for intramolecular conformational optimization. 2. Tests on the homopolypeptides decaglycine and icosalanine, J. Phys. Chem. 97: 260-266.
    • (1993) J. Phys. Chem. , vol.97 , pp. 260-266
    • Olszewski, K.A.1    Piela, L.2    Scheraga, H.A.3
  • 56
    • 0039790361 scopus 로고
    • Mean field theory as a tool for intramolecular conformational optimization. 3. Test on melittin
    • Olszewski, K.A., Piela, L. and Scheraga, H.A. (1993), Mean field theory as a tool for intramolecular conformational optimization. 3. Test on melittin, J. Phys. Chem. 97: 267-270.
    • (1993) J. Phys. Chem. , vol.97 , pp. 267-270
    • Olszewski, K.A.1    Piela, L.2    Scheraga, H.A.3
  • 57
    • 0000594925 scopus 로고
    • The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method
    • Piela, L., Kostrowicki, J. and Scheraga, H.A. (1989), The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method, J. Phys. Chem. 93: 3339-3346.
    • (1989) J. Phys. Chem. , vol.93 , pp. 3339-3346
    • Piela, L.1    Kostrowicki, J.2    Scheraga, H.A.3
  • 58
    • 0000674852 scopus 로고
    • Performance of the shift method of global minimization in searches for optimum structures of clusters of Lennard-Jones atoms
    • Pillardy, J., Olszewski, K.A. and Piela, L. (1992), Performance of the shift method of global minimization in searches for optimum structures of clusters of Lennard-Jones atoms, J. Phys. Chem. 96: 4337-4341.
    • (1992) J. Phys. Chem. , vol.96 , pp. 4337-4341
    • Pillardy, J.1    Olszewski, K.A.2    Piela, L.3
  • 59
    • 0000771215 scopus 로고
    • Molecular dynamics on deformed potential energy hypersurfaces
    • Pillardy, J. and Piela, L. (1995), Molecular dynamics on deformed potential energy hypersurfaces, J. Phys. Chem. 99: 11805-11812.
    • (1995) J. Phys. Chem. , vol.99 , pp. 11805-11812
    • Pillardy, J.1    Piela, L.2
  • 61
    • 0001448076 scopus 로고    scopus 로고
    • Diffusion equation and distance scaling methods of global optimization; Applications to crystal structure prediction
    • Wawak, R.J., Pillardy, J., Liwo, A., Gibson, K.D. and Scheraga, H.A. (1998), Diffusion equation and distance scaling methods of global optimization; Applications to crystal structure prediction, J. Phys. Chem. 102: 2904-2918.
    • (1998) J. Phys. Chem. , vol.102 , pp. 2904-2918
    • Wawak, R.J.1    Pillardy, J.2    Liwo, A.3    Gibson, K.D.4    Scheraga, H.A.5
  • 62
    • 0001756405 scopus 로고    scopus 로고
    • An efficient deformation-based global optimization method for off-lattice polymer chains; self-consistent basin-to-deformed-basin mapping (SCBDBM). Application to united-residue polypeptide chains
    • Pillardy, J., Liwo, A., Groth, M. and Scheraga, H.A., An efficient deformation-based global optimization method for off-lattice polymer chains; self-consistent basin-to-deformed-basin mapping (SCBDBM). Application to united-residue polypeptide chains, J. Phys. Chem. B103: 7353-7366.
    • J. Phys. Chem. , vol.103 B , pp. 7353-7366
    • Pillardy, J.1    Liwo, A.2    Groth, M.3    Scheraga, H.A.4
  • 63
    • 0000625567 scopus 로고    scopus 로고
    • An efficient deformation-based global optimization method [self-consistent basin-to-deformed-basin mapping (SCBDBM)]; Application to Lennard-Jones atomic clusters
    • in press
    • Pillardy, J., Liwo, A. and Scheraga, H.A. An efficient deformation-based global optimization method [self-consistent basin-to-deformed-basin mapping (SCBDBM)]; Application to Lennard-Jones atomic clusters, J. Phys. Chem., in press.
    • J. Phys. Chem.
    • Pillardy, J.1    Liwo, A.2    Scheraga, H.A.3
  • 64
    • 0001425721 scopus 로고
    • Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones atoms
    • Kostrowicki, J., Piela, L., Cherayil, B.J. and Scheraga, H.A. (1991), Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones atoms, J. Phys. Chem. 95: 4113-4119.
    • (1991) J. Phys. Chem. , vol.95 , pp. 4113-4119
    • Kostrowicki, J.1    Piela, L.2    Cherayil, B.J.3    Scheraga, H.A.4
  • 65
    • 0001031117 scopus 로고
    • Application of the diffusion equation method of global optimization to water clusters
    • Wawak, R.J., Wimmer, M.M. and Scheraga, H.A. (1992), Application of the diffusion equation method of global optimization to water clusters, J. Phys. Chem. 96: 5138-5145.
    • (1992) J. Phys. Chem. , vol.96 , pp. 5138-5145
    • Wawak, R.J.1    Wimmer, M.M.2    Scheraga, H.A.3
  • 66
    • 0001031118 scopus 로고
    • Application of the diffusion equation method for global optimization to oligopeptides
    • Kostrowicki, J. and Scheraga, H.A. (1992), Application of the diffusion equation method for global optimization to oligopeptides, J. Phys. Chem. 96: 7442-7449.
    • (1992) J. Phys. Chem. , vol.96 , pp. 7442-7449
    • Kostrowicki, J.1    Scheraga, H.A.2
  • 67
    • 0000542341 scopus 로고
    • Theoretically predicted lowest-energy structures of water clusters
    • Pillardy, J., Olszewski, K.A. and Piela, L. (1992), Theoretically predicted lowest-energy structures of water clusters, J. Mol. Struct. 270: 277-285.
    • (1992) J. Mol. Struct. , vol.270 , pp. 277-285
    • Pillardy, J.1    Olszewski, K.A.2    Piela, L.3
  • 68
    • 0001176785 scopus 로고    scopus 로고
    • New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
    • Lee, J., Scheraga, H.A. and Rackovsky, S. (1997), New optimization method for conformational energy calculations on polypeptides: Conformational space annealing, J. Comput. Chem. 18: 1222-1232.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1222-1232
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 69
    • 0032146482 scopus 로고    scopus 로고
    • Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing
    • Lee, J., Scheraga, H.A. and Rackovsky, S. (1998), Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing, Biopolymers 46: 103-115.
    • (1998) Biopolymers , vol.46 , pp. 103-115
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 70
    • 0000542451 scopus 로고    scopus 로고
    • Conformational space annealing by parallel computations: Extensive conformational search of Met-enkephalin and of the 20-residue membrane-bound portion of melittin
    • Lee, J. and Scheraga, H.A. (1999), Conformational space annealing by parallel computations: extensive conformational search of Met-enkephalin and of the 20-residue membrane-bound portion of melittin, Int. J. Quant. Chem. 75: 255-265.
    • (1999) Int. J. Quant. Chem. , vol.75 , pp. 255-265
    • Lee, J.1    Scheraga, H.A.2
  • 72
    • 0033514939 scopus 로고    scopus 로고
    • Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein a and to apo calbindin D9K
    • Lee, J., Liwo, A. and Scheraga, H.A. (1999), Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K., Proc. Natl. Acad. Sci. USA 96: 2025-2030.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 2025-2030
    • Lee, J.1    Liwo, A.2    Scheraga, H.A.3
  • 73
    • 0013302029 scopus 로고    scopus 로고
    • Kinetics of protein folding
    • "Slow Dynamics in Complex Systems: Eighth Tohwa University International Symposium", Eds. M. Tokuyama and I. Oppenheim Amer. Inst. Phys.
    • Ye, Y.-J. and Scheraga, H.A. (1999), Kinetics of protein folding, in "Slow Dynamics in Complex Systems: Eighth Tohwa University International Symposium", Eds. M. Tokuyama and I. Oppenheim. AIP Conference Proceedings 469, pp. 452-475, Amer. Inst. Phys.
    • (1999) AIP Conference Proceedings , vol.469 , pp. 452-475
    • Ye, Y.-J.1    Scheraga, H.A.2
  • 74
    • 0032845539 scopus 로고    scopus 로고
    • Kinetics of cooperative protein folding involving two separate conformational families
    • Ye, Y.-J., Ripoll, D.R. and Scheraga, H.A. (1999), Kinetics of cooperative protein folding involving two separate conformational families, Computational and Theoretical Polymer Science, 9: 359-370.
    • (1999) Computational and Theoretical Polymer Science , vol.9 , pp. 359-370
    • Ye, Y.-J.1    Ripoll, D.R.2    Scheraga, H.A.3
  • 75
    • 0033545962 scopus 로고    scopus 로고
    • Protein structure can be predicted by global optimization of a potential energy function
    • Liwo, A., Lee, J., Ripoll, D.R., Pillardy, J. and Scheraga, H.A. (1999), Protein structure can be predicted by global optimization of a potential energy function, Proc. Natl. Acad. Sci., USA, 96: 5482-5485.
    • (1999) Proc. Natl. Acad. Sci., USA , vol.96 , pp. 5482-5485
    • Liwo, A.1    Lee, J.2    Ripoll, D.R.3    Pillardy, J.4    Scheraga, H.A.5
  • 76
    • 0002336164 scopus 로고
    • Ring closure and local conformational deformations of chain molecules
    • Go, N. and Scheraga, H.A. (1970), Ring closure and local conformational deformations of chain molecules, Macromolecules 3: 178-187.
    • (1970) Macromolecules , vol.3 , pp. 178-187
    • Go, N.1    Scheraga, H.A.2
  • 77
    • 84986437139 scopus 로고
    • Standard-geometry chains fitted to X-ray derived structures; Validation of the rigid-geometry approximation. I. Chain closure through a limited search of 'loop' conformations
    • Palmer, K.A. and Scheraga, H.A. (1991), Standard-geometry chains fitted to X-ray derived structures; Validation of the rigid-geometry approximation. I. Chain closure through a limited search of 'loop' conformations, J. Comput. Chem. 12: 505-526.
    • (1991) J. Comput. Chem. , vol.12 , pp. 505-526
    • Palmer, K.A.1    Scheraga, H.A.2
  • 78
    • 0026076082 scopus 로고
    • Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor
    • Vila, J., Williams, R.L., Vásquez, M. and Scheraga, H.A. (1991), Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor, Proteins: Struc., Func., and Gen. 10: 199-218.
    • (1991) Proteins: Struc., Func., and Gen. , vol.10 , pp. 199-218
    • Vila, J.1    Williams, R.L.2    Vásquez, M.3    Scheraga, H.A.4
  • 80
    • 0032605909 scopus 로고    scopus 로고
    • Calculation of protein conformation by global optimization of a potential energy function
    • Lee, J., Liwo, A., Ripoll, D.R., Pillardy, J. and Scheraga, H.A. (1999), Calculation of protein conformation by global optimization of a potential energy function, Proteins: Struc., Func., and Gen., suppl. 3: 204-208.
    • (1999) Proteins: Struc., Func., and Gen. , Issue.3 SUPPL. , pp. 204-208
    • Lee, J.1    Liwo, A.2    Ripoll, D.R.3    Pillardy, J.4    Scheraga, H.A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.