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Volumn 7, Issue 3, 1998, Pages 649-666

Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin

Author keywords

Conformational space; Dimensionality reduction; Ergodicity; Molecular dynamics simulation; Multiple minima; Potential energy surface; Principal components analysis; Sensitivity to initial conditions

Indexed keywords

NUCLEIC ACID; PROTEIN;

EID: 0031910020     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070314     Document Type: Article
Times cited : (429)

References (99)
  • 4
    • 0028869415 scopus 로고
    • Multiple molecular-dynamics simulations of the anticodon loop of tRNA(ASP) in aqueous-solution with counterions
    • Auffinger P, Louise-May S, Westhof E. 1995. Multiple molecular-dynamics simulations of the anticodon loop of tRNA(ASP) in aqueous-solution with counterions. J Am Chem Soc 117:6720-6726.
    • (1995) J Am Chem Soc , vol.117 , pp. 6720-6726
    • Auffinger, P.1    Louise-May, S.2    Westhof, E.3
  • 5
    • 0029776466 scopus 로고    scopus 로고
    • H-bond stability in the tRNA(ASP) anticodon hairpin: 3 ns of multiple molecular dynamics simulations
    • Auffinger P, Westhof E. 1996. H-bond stability in the tRNA(ASP) anticodon hairpin: 3 ns of multiple molecular dynamics simulations. Biophys J 71:940-954.
    • (1996) Biophys J , vol.71 , pp. 940-954
    • Auffinger, P.1    Westhof, E.2
  • 6
    • 0031566427 scopus 로고    scopus 로고
    • RNA Hydration: Three ns of multiple molecular dynamics simulations of solvated tRNA(ASP) anticodon hairpin
    • Auffinger P, Westhof E. 1997. RNA Hydration: Three ns of multiple molecular dynamics simulations of solvated tRNA(ASP) anticodon hairpin. J Mol Biol 269:326-341.
    • (1997) J Mol Biol , vol.269 , pp. 326-341
    • Auffinger, P.1    Westhof, E.2
  • 7
    • 0002150724 scopus 로고
    • Molecular dynamics simulations of supercooled liquids near the glass transition
    • Barrat JL, Klein ML. 1991. Molecular dynamics simulations of supercooled liquids near the glass transition. Ann Rev Phys Chem 42:23-53.
    • (1991) Ann Rev Phys Chem , vol.42 , pp. 23-53
    • Barrat, J.L.1    Klein, M.L.2
  • 8
    • 0000370391 scopus 로고    scopus 로고
    • The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
    • Becker OM, Karplus M. 1997. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics. J Chem Phys 106:1495-1517.
    • (1997) J Chem Phys , vol.106 , pp. 1495-1517
    • Becker, O.M.1    Karplus, M.2
  • 10
    • 0030021471 scopus 로고    scopus 로고
    • Biomolecular dynamics comes of age
    • Berendsen HJC. 1996. Biomolecular dynamics comes of age. Science 271:954-955.
    • (1996) Science , vol.271 , pp. 954-955
    • Berendsen, H.J.C.1
  • 11
    • 0030904524 scopus 로고    scopus 로고
    • Novel methods of sampling phase space in the simulation of biological systems
    • Berne BJ, Straub JE. 1997. Novel methods of sampling phase space in the simulation of biological systems. Curr Opin Struct Biol 7:181-189.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 181-189
    • Berne, B.J.1    Straub, J.E.2
  • 13
    • 0029151245 scopus 로고
    • First principles calculation of the folding free energy of a 3-helix bundle protein
    • Boczko EM, Brooks CL. 1995. First principles calculation of the folding free energy of a 3-helix bundle protein. Science 269:393-396.
    • (1995) Science , vol.269 , pp. 393-396
    • Boczko, E.M.1    Brooks, C.L.2
  • 14
    • 0027474781 scopus 로고
    • Ensemble iterative relaxation matrix approach - A new NMR refinement protocol applied to the solution structure of crambin
    • Bonvin AMJJ, Rullmann JAC, Lamerichs RMJN, Boelens R, Kaptein R. 1993. Ensemble iterative relaxation matrix approach - A new NMR refinement protocol applied to the solution structure of crambin. Proteins Struct Funct Genet 15:385-400.
    • (1993) Proteins Struct Funct Genet , vol.15 , pp. 385-400
    • Bonvin, A.M.J.J.1    Rullmann, J.A.C.2    Lamerichs, R.M.J.N.3    Boelens, R.4    Kaptein, R.5
  • 16
    • 0029000691 scopus 로고
    • Methodological advances in molecular dynamics simulations of biological systems
    • Brooks CL III. 1995. Methodological advances in molecular dynamics simulations of biological systems. Curr Opin Struct Biol 5:211-215.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 211-215
    • Brooks III, C.L.1
  • 18
    • 0025294114 scopus 로고
    • Conformational sampling using high-temperature molecular-dynamics
    • Bruccoleri RE, Karplus M. 1990. Conformational sampling using high-temperature molecular-dynamics. Biopolymers 29:1847-1862.
    • (1990) Biopolymers , vol.29 , pp. 1847-1862
    • Bruccoleri, R.E.1    Karplus, M.2
  • 19
    • 0002574639 scopus 로고
    • Molecular dynamics simulations with experimental restraints
    • Brunger AT, Karplus M. 1991. Molecular dynamics simulations with experimental restraints. Acc Chem Res 24:54-61.
    • (1991) Acc Chem Res , vol.24 , pp. 54-61
    • Brunger, A.T.1    Karplus, M.2
  • 20
    • 0029644475 scopus 로고
    • Problems in simulating macromolecular movements
    • Caspar D. 1995. Problems in simulating macromolecular movements. Structure 3:327-329.
    • (1995) Structure , vol.3 , pp. 327-329
    • Caspar, D.1
  • 21
  • 22
    • 0029941154 scopus 로고    scopus 로고
    • Observation of the A-DNA to B-DNA transition during unrestrained molecular-dynamics in aqueous-solution
    • Cheatham TE, Kollman PA. 1996. Observation of the A-DNA to B-DNA transition during unrestrained molecular-dynamics in aqueous-solution. J Mol Biol 259:434-444.
    • (1996) J Mol Biol , vol.259 , pp. 434-444
    • Cheatham, T.E.1    Kollman, P.A.2
  • 24
    • 24844461839 scopus 로고    scopus 로고
    • Using phase-portraits to visualize sub-states, sampling, and chaos in protein dynamics
    • Clarage JB, Romo TD, Andrews BK, Pettitt BM, Phillips GN. 1996. Using phase-portraits to visualize sub-states, sampling, and chaos in protein dynamics. Biophys J 70:MPMC1-MPMC1.
    • (1996) Biophys J , vol.70
    • Clarage, J.B.1    Romo, T.D.2    Andrews, B.K.3    Pettitt, B.M.4    Phillips, G.N.5
  • 25
    • 0000725483 scopus 로고
    • Thermodynamic fluctuations in protein molecules
    • Cooper A. 1976. Thermodynamic fluctuations in protein molecules. Proc Natl Acad Sci USA 73:2740-2741.
    • (1976) Proc Natl Acad Sci USA , vol.73 , pp. 2740-2741
    • Cooper, A.1
  • 26
    • 0000191981 scopus 로고
    • Reaction path study of conformational transitions in flexible systems - Applications to peptides
    • Czerminski R, Elber R. 1990. Reaction path study of conformational transitions in flexible systems - Applications to peptides. J Chem Phys 92:5580-5601.
    • (1990) J Chem Phys , vol.92 , pp. 5580-5601
    • Czerminski, R.1    Elber, R.2
  • 27
    • 0027256738 scopus 로고
    • Realistic simulations of native-protein dynamics in solution and beyond
    • Daggett V, Levitt M. 1993. Realistic simulations of native-protein dynamics in solution and beyond. Ann Rev Biophys Biomol Struc 22:353-380.
    • (1993) Ann Rev Biophys Biomol Struc , vol.22 , pp. 353-380
    • Daggett, V.1    Levitt, M.2
  • 28
    • 0029993330 scopus 로고    scopus 로고
    • On the sensitivity of MD trajectories to changes in water-protein interaction parameters: The potato carboxypeptidase inhibitor in water asa test case for the GROMOS force field
    • Daura X, Oliva B, Querol E, Aviles FX, Tapia O. 1996. On the sensitivity of MD trajectories to changes in water-protein interaction parameters: The potato carboxypeptidase inhibitor in water asa test case for the GROMOS force field. Proteins Struct Funct Genet 25:89-103.
    • (1996) Proteins Struct Funct Genet , vol.25 , pp. 89-103
    • Daura, X.1    Oliva, B.2    Querol, E.3    Aviles, F.X.4    Tapia, O.5
  • 31
    • 0029052930 scopus 로고
    • Long timestep dynamics of peptides by the dynamics driver approach
    • Derremaux P, Schlick T. 1995. Long timestep dynamics of peptides by the dynamics driver approach. Proteins Struct Funct Genet 21:282-302.
    • (1995) Proteins Struct Funct Genet , vol.21 , pp. 282-302
    • Derremaux, P.1    Schlick, T.2
  • 32
    • 0010915520 scopus 로고
    • Protein molecular dynamics constrained to slow modes: Theoretical approach based on a hierarchy of modes with a set of holonomic constraints - The methods and its tests on citrate synthase
    • Durup J. 1991. Protein molecular dynamics constrained to slow modes: Theoretical approach based on a hierarchy of modes with a set of holonomic constraints - The methods and its tests on citrate synthase. J Phys Chem 95:1817-1829.
    • (1991) J Phys Chem , vol.95 , pp. 1817-1829
    • Durup, J.1
  • 33
    • 0023140044 scopus 로고
    • Multiple conformational states of proteins - A molecular-dynamics analysis of myoglobin
    • Elber R, Karplus M. 1987. Multiple conformational states of proteins - A molecular-dynamics analysis of myoglobin. Science 235:318-321.
    • (1987) Science , vol.235 , pp. 318-321
    • Elber, R.1    Karplus, M.2
  • 34
    • 0025600834 scopus 로고
    • Enhanced sampling in molecular-dynamics - Use of the time-dependent hartree approximation for a simulation of carbonmonoxide diffusion through myoglobin
    • Elber R, Karplus M. 1990. Enhanced sampling in molecular-dynamics - Use of the time-dependent hartree approximation for a simulation of carbonmonoxide diffusion through myoglobin. J Am Chem Soc 112:9161-9175.
    • (1990) J Am Chem Soc , vol.112 , pp. 9161-9175
    • Elber, R.1    Karplus, M.2
  • 35
    • 0027366431 scopus 로고
    • How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized E. coli thioredoxin
    • Elofsson A, Nilsson L. 1993. How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized E. coli thioredoxin. J Mol Biol 233:766-780.
    • (1993) J Mol Biol , vol.233 , pp. 766-780
    • Elofsson, A.1    Nilsson, L.2
  • 38
  • 39
    • 0026320866 scopus 로고
    • The energy landscape and motions of proteins
    • Frauenfelder H, Sligar SG, Wolynes PG. 1991. The energy landscape and motions of proteins. Science 254:1598-1603.
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 40
    • 0002237761 scopus 로고
    • Biomolecules: Where the physics of complexity and simplicity meet
    • Frauenfelder H, Wolynes PG. 1994. Biomolecules: Where the physics of complexity and simplicity meet. Physics Today 47:58-64.
    • (1994) Physics Today , vol.47 , pp. 58-64
    • Frauenfelder, H.1    Wolynes, P.G.2
  • 41
    • 0000577041 scopus 로고
    • Large-amplitude nonlinear motions in proteins
    • Garcia AE. 1992. Large-amplitude nonlinear motions in proteins. Phys Rev Lett 68:2696-2699.
    • (1992) Phys Rev Lett , vol.68 , pp. 2696-2699
    • Garcia, A.E.1
  • 42
    • 0011479901 scopus 로고
    • Multi-basin dynamics of a protein in aqueous solution
    • Peyrard M, ed. New York: Springer
    • Garcia AE. 1995. Multi-basin dynamics of a protein in aqueous solution. In: Peyrard M, ed. Nonlinear excitations in biomolecules. New York: Springer, pp 191-206.
    • (1995) Nonlinear Excitations in Biomolecules , pp. 191-206
    • Garcia, A.E.1
  • 43
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein M, Lesk AM, Chothia C. 1994. Structural mechanisms for domain movements in proteins. Biochemistry 33:6739-6749.
    • (1994) Biochemistry , vol.33 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 46
    • 0028292635 scopus 로고
    • Harmonic and anharmonic aspects in the dynamics of BPTI - A normal mode analysis and principal component analysis
    • Hayward S, Kitao A, Go N. 1994. Harmonic and anharmonic aspects in the dynamics of BPTI - A normal mode analysis and principal component analysis. Protein Sci 3:936-943.
    • (1994) Protein Sci , vol.3 , pp. 936-943
    • Hayward, S.1    Kitao, A.2    Go, N.3
  • 47
    • 0027732618 scopus 로고
    • Effect of solvent on collective motions in globular protein
    • Hayward S, Kitao A, Hirata F, Go N. 1993. Effect of solvent on collective motions in globular protein. J Mol Biol 234:1207-1217.
    • (1993) J Mol Biol , vol.234 , pp. 1207-1217
    • Hayward, S.1    Kitao, A.2    Hirata, F.3    Go, N.4
  • 48
    • 0019450355 scopus 로고
    • Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulfur
    • Hendrickson WA, Teeter MM. 1981. Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulfur. Nature 290:107-113.
    • (1981) Nature , vol.290 , pp. 107-113
    • Hendrickson, W.A.1    Teeter, M.M.2
  • 50
    • 0000441039 scopus 로고
    • Conformational substates and uncertainty in macromolecular free energy calculations
    • Hodel A, Simonson T, Fox RO, Brunger AT 1993. Conformational substates and uncertainty in macromolecular free energy calculations. J Phys Chem 97:3409-3417.
    • (1993) J Phys Chem , vol.97 , pp. 3409-3417
    • Hodel, A.1    Simonson, T.2    Fox, R.O.3    Brunger, A.T.4
  • 51
    • 0029092698 scopus 로고
    • Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular-dynamics simulations
    • Hunenberger PH, Mark AE, van Gunsteren WF. 1995. Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular-dynamics simulations. J Mol Biol 252:492-503.
    • (1995) J Mol Biol , vol.252 , pp. 492-503
    • Hunenberger, P.H.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 52
    • 0023512803 scopus 로고
    • Anisotropy and anharmonicity of atomic fluctuations in proteins: Analysis of a molecular-dynamics simulation
    • Ichiye T, Karplus M. 1987. Anisotropy and anharmonicity of atomic fluctuations in proteins: Analysis of a molecular-dynamics simulation. Proteins Struct Funct Genet 2:236-259.
    • (1987) Proteins Struct Funct Genet , vol.2 , pp. 236-259
    • Ichiye, T.1    Karplus, M.2
  • 53
    • 0024276807 scopus 로고
    • Anisotropy and anharmonicity of atomic fluctuations in proteins: Implications for X-ray-analysis
    • Ichiye T, Karplus M. 1988. Anisotropy and anharmonicity of atomic fluctuations in proteins: Implications for X-ray-analysis. Biochemistry 27:3487-3497.
    • (1988) Biochemistry , vol.27 , pp. 3487-3497
    • Ichiye, T.1    Karplus, M.2
  • 55
    • 33645941402 scopus 로고
    • The OPLS potential functions for proteins -Energy minimizations for crystals of cyclic-peptides and crambin
    • Jorgensen WL, Tirado-Rives J. 1988. The OPLS potential functions for proteins -Energy minimizations for crystals of cyclic-peptides and crambin. J Am Chem Soc 110:1666-1671.
    • (1988) J Am Chem Soc , vol.110 , pp. 1666-1671
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 56
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • Kabsch W. 1978. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Cryst A34:827-828.
    • (1978) Acta Cryst , vol.A34 , pp. 827-828
    • Kabsch, W.1
  • 57
    • 0025048105 scopus 로고
    • Molecular dynamics simulations in biology
    • Karplus M, Petsko GA. 1990. Molecular dynamics simulations in biology. Nature 347:631-639.
    • (1990) Nature , vol.347 , pp. 631-639
    • Karplus, M.1    Petsko, G.A.2
  • 59
    • 0025328145 scopus 로고
    • Temperature-dependence of the structure and dynamics of myoglobin - A simulation approach
    • Kuczera K, Kuriyan J, Karplus M. 1990. Temperature-dependence of the structure and dynamics of myoglobin - A simulation approach. J Mol Biol 213:351-373.
    • (1990) J Mol Biol , vol.213 , pp. 351-373
    • Kuczera, K.1    Kuriyan, J.2    Karplus, M.3
  • 60
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method
    • Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method. J Comput Chem 13:1011-1021.
    • (1992) J Comput Chem , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 61
    • 84986497803 scopus 로고
    • Multi-dimensional free energy calculations using the weighted histogram analysis method
    • Kumar S, Rosenberg JM, Bouzida D, Swendsen RH, Kollman PA. 1995. Multi-dimensional free energy calculations using the weighted histogram analysis method. J Comput Chem 16:1339-1350.
    • (1995) J Comput Chem , vol.16 , pp. 1339-1350
    • Kumar, S.1    Rosenberg, J.M.2    Bouzida, D.3    Swendsen, R.H.4    Kollman, P.A.5
  • 62
    • 0021104755 scopus 로고
    • Molecular dynamics of native protein: II Analysis and nature of motion
    • Levitt M. 1985. Molecular dynamics of native protein: II Analysis and nature of motion. J Mol Biol 168:621-657.
    • (1985) J Mol Biol , vol.168 , pp. 621-657
    • Levitt, M.1
  • 63
    • 0024094768 scopus 로고
    • Accurate simulation of protein dynamics in solution
    • Levitt M, Sharon R. 1988. Accurate simulation of protein dynamics in solution. Proc Natl Acad Sci USA 85:7557-7562.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 7557-7562
    • Levitt, M.1    Sharon, R.2
  • 64
    • 0000961995 scopus 로고
    • Evaluation of the configurational entropy for proteins - Application to molecular-dynamics simulations of an alpha-helix
    • Levy RM, Karplus M, Kushick J, Perahia D. 1984. Evaluation of the configurational entropy for proteins - Application to molecular-dynamics simulations of an alpha-helix. Macromolecules 17:1370-1374.
    • (1984) Macromolecules , vol.17 , pp. 1370-1374
    • Levy, R.M.1    Karplus, M.2    Kushick, J.3    Perahia, D.4
  • 65
    • 0000579428 scopus 로고
    • Molecular-dynamics of an alpha-helical polypeptide: Temperature-dependence and deviation from harmonic behavior
    • Levy RM, Perahia D, Karplus M. 1982. Molecular-dynamics of an alpha-helical polypeptide: Temperature-dependence and deviation from harmonic behavior. Proc Natl Acad Sci USA 79:1346-1350.
    • (1982) Proc Natl Acad Sci USA , vol.79 , pp. 1346-1350
    • Levy, R.M.1    Perahia, D.2    Karplus, M.3
  • 68
    • 0026048380 scopus 로고
    • Mass-weighted molecular dynamics simulations and conformational analysis of polypeptide
    • Mao B. 1991. Mass-weighted molecular dynamics simulations and conformational analysis of polypeptide. Biophys J 60:611-622.
    • (1991) Biophys J , vol.60 , pp. 611-622
    • Mao, B.1
  • 70
    • 0012181565 scopus 로고
    • Measures of effective ergodic convergence in liquids
    • Mountain RD, Thirumalai D. 1989. Measures of effective ergodic convergence in liquids. J Phys Chem 93:6975-6979.
    • (1989) J Phys Chem , vol.93 , pp. 6975-6979
    • Mountain, R.D.1    Thirumalai, D.2
  • 71
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free-energies in molecular-systems
    • Neria E, Fischer S, Karplus M. 1996. Simulation of activation free-energies in molecular-systems. J Chem Phys 105:1902-1921.
    • (1996) J Chem Phys , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 72
    • 0024585391 scopus 로고
    • Structural basis of hierarchical multiple substates of a protein - Introduction
    • Noguti T, Go N. 1989. Structural basis of hierarchical multiple substates of a protein - Introduction. Proteins Struct Funct Genet 5:97-103.
    • (1989) Proteins Struct Funct Genet , vol.5 , pp. 97-103
    • Noguti, T.1    Go, N.2
  • 73
    • 6244306010 scopus 로고
    • Liquid water dynamics: Collective motions, fluctuation and relaxation
    • Ohmine I. 1995. Liquid water dynamics: Collective motions, fluctuation and relaxation. J Phys Chem 99:6767-6776.
    • (1995) J Phys Chem , vol.99 , pp. 6767-6776
    • Ohmine, I.1
  • 74
    • 0025280347 scopus 로고
    • Using molecular dynamics simulations of crambin to evaluate the suitability of different continuum dielectric and hydrogen-atom models for protein simulations
    • Omstein RCJ. 1990. Using molecular dynamics simulations of crambin to evaluate the suitability of different continuum dielectric and hydrogen-atom models for protein simulations. J Biomol Struct Dynam 7:1019-1041.
    • (1990) J Biomol Struct Dynam , vol.7 , pp. 1019-1041
    • Omstein, R.C.J.1
  • 75
  • 76
    • 0024953088 scopus 로고
    • Mechanisms of cooperativity and allosteric regulation in proteins
    • Perutz MF. 1989. Mechanisms of cooperativity and allosteric regulation in proteins. Quart Rev Biophys 22:139-236.
    • (1989) Quart Rev Biophys , vol.22 , pp. 139-236
    • Perutz, M.F.1
  • 77
    • 0029972976 scopus 로고    scopus 로고
    • Not just your average structures
    • Petsko GA. 1996. Not just your average structures. Nature Struct Biol 3:565-566.
    • (1996) Nature Struct Biol , vol.3 , pp. 565-566
    • Petsko, G.A.1
  • 78
    • 0023042577 scopus 로고
    • Molecular-dynamics simulations of native and substrate-bound lysozyme - A study of the average structures and atomic fluctuations
    • Post CB, Brooks BR, Karplus M, Dobson CM, Artymiuk PJ, Cheetham JC, Phillips DC. 1986. Molecular-dynamics simulations of native and substrate-bound lysozyme - A study of the average structures and atomic fluctuations. J Mol Biol 190:455-479.
    • (1986) J Mol Biol , vol.190 , pp. 455-479
    • Post, C.B.1    Brooks, B.R.2    Karplus, M.3    Dobson, C.M.4    Artymiuk, P.J.5    Cheetham, J.C.6    Phillips, D.C.7
  • 79
    • 0021902413 scopus 로고
    • Mapping protein dynamics by X-ray diffraction
    • Ringe D, Petsko GA. 1985. Mapping protein dynamics by X-ray diffraction. Prog Biophys Mol Biol 45:197-235.
    • (1985) Prog Biophys Mol Biol , vol.45 , pp. 197-235
    • Ringe, D.1    Petsko, G.A.2
  • 80
    • 0003933104 scopus 로고
    • Princeton, New Jersey: Princeton University Press
    • Ruelle D. 1991. Chance and chaos. Princeton, New Jersey: Princeton University Press.
    • (1991) Chance and Chaos
    • Ruelle, D.1
  • 81
    • 0029820258 scopus 로고    scopus 로고
    • Structural stability of disulphide mutants of basic pancreatic trypsin inhibitor: A molecular dynamics study
    • Schiffer CA, van Gunsteren WF. 1996. Structural stability of disulphide mutants of basic pancreatic trypsin inhibitor: A molecular dynamics study. Proteins 26:66-71.
    • (1996) Proteins , vol.26 , pp. 66-71
    • Schiffer, C.A.1    Van Gunsteren, W.F.2
  • 82
    • 0001732911 scopus 로고
    • Stochastic dynamics simulations of the alanine dipeptide using a solvent modified potential energy surface
    • Smith PE, Pettit BM, Karplus M. 1993. Stochastic dynamics simulations of the alanine dipeptide using a solvent modified potential energy surface. J Phys Chem 97:6907-6913.
    • (1993) J Phys Chem , vol.97 , pp. 6907-6913
    • Smith, P.E.1    Pettit, B.M.2    Karplus, M.3
  • 84
    • 0042091834 scopus 로고
    • Packing structures and transitions in liquids and solids
    • Stillinger FH, Weber TA. 1984. Packing structures and transitions in liquids and solids. Science 225:983-989.
    • (1984) Science , vol.225 , pp. 983-989
    • Stillinger, F.H.1    Weber, T.A.2
  • 85
    • 0027972206 scopus 로고
    • Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease A
    • Straub JE, Rashkin AB, Thirumalai D. 1994. Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease A. J Am Chem Soc 116:2049-2063.
    • (1994) J Am Chem Soc , vol.116 , pp. 2049-2063
    • Straub, J.E.1    Rashkin, A.B.2    Thirumalai, D.3
  • 86
    • 0027502502 scopus 로고
    • Theoretical probes of conformational fluctuations in S-peptide and RNase A/3′-UMP enzyme product complex
    • Straub JE, Thirumalai D. 1993. Theoretical probes of conformational fluctuations in S-peptide and RNase A/3′-UMP enzyme product complex. Proteins Struct Funct Genet 15:360-373.
    • (1993) Proteins Struct Funct Genet , vol.15 , pp. 360-373
    • Straub, J.E.1    Thirumalai, D.2
  • 87
    • 0000118827 scopus 로고
    • Harmonic and quasiharmonic descriptions of crambin
    • Teeter MM, Case DA. 1990. Harmonic and quasiharmonic descriptions of crambin. J Phys Chem 94:8091-8097.
    • (1990) J Phys Chem , vol.94 , pp. 8091-8097
    • Teeter, M.M.1    Case, D.A.2
  • 88
    • 0027390460 scopus 로고
    • The contribution of cross-links to protein stability - A normal mode analysis of the configurational entropy of the native-state
    • Tidor B, Karplus M. 1993. The contribution of cross-links to protein stability - A normal mode analysis of the configurational entropy of the native-state. Proteins Struct Funct Genet 15:71-79.
    • (1993) Proteins Struct Funct Genet , vol.15 , pp. 71-79
    • Tidor, B.1    Karplus, M.2
  • 90
    • 0029152775 scopus 로고
    • Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory
    • Trover JM, Cohen FE. 1995. Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory. Proteins Struct Funct Genet 23:97-110.
    • (1995) Proteins Struct Funct Genet , vol.23 , pp. 97-110
    • Trover, J.M.1    Cohen, F.E.2
  • 92
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constrained dynamics
    • van Gunsteren WF, Berendsen HJC. 1977. Algorithms for macromolecular dynamics and constrained dynamics. Mol Phys 34:1311-1327.
    • (1977) Mol Phys , vol.34 , pp. 1311-1327
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 94
    • 0026843945 scopus 로고
    • Conformational search by potential-energy annealing - Algorithm and application to cyclosporin A
    • van Schaik RC, van Gunsteren WF, Berendsen HJC. 1992. Conformational search by potential-energy annealing - Algorithm and application to cyclosporin A. J Comput-Aided Mol Design 6:97-112.
    • (1992) J Comput-Aided Mol Design , vol.6 , pp. 97-112
    • Van Schaik, R.C.1    Van Gunsteren, W.F.2    Berendsen, H.J.C.3
  • 95
    • 0001183716 scopus 로고
    • Simulations of macromolecules by multiple time-step methods
    • Watanabe M, Karplus M. 1995. Simulations of macromolecules by multiple time-step methods. J Phys Chem 99:5680-5697.
    • (1995) J Phys Chem , vol.99 , pp. 5680-5697
    • Watanabe, M.1    Karplus, M.2
  • 96
    • 0001658242 scopus 로고
    • An empirical-examination of potential-energy minimization using the well-determined structure of the protein crambin
    • Whitlow M, Teeter MM. 1986. An empirical-examination of potential-energy minimization using the well-determined structure of the protein crambin. J Am Chem Soc 108:7163-7172.
    • (1986) J Am Chem Soc , vol.108 , pp. 7163-7172
    • Whitlow, M.1    Teeter, M.M.2
  • 97
    • 0029823282 scopus 로고    scopus 로고
    • Rational choice of molecular dynamics simulation parameters through the use of three-dimensional autocorrelation method: Application to calmodulin flexibility study
    • Yasri A, Chiche L, Haiech J, Grassy G. 1996. Rational choice of molecular dynamics simulation parameters through the use of three-dimensional autocorrelation method: Application to calmodulin flexibility study. Protein Eng 9:959-976.
    • (1996) Protein Eng , vol.9 , pp. 959-976
    • Yasri, A.1    Chiche, L.2    Haiech, J.3    Grassy, G.4
  • 98
    • 36449007976 scopus 로고
    • The effect of long-range interactions in the simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
    • York DM, Darden TA, Pedersen LG. 1993. The effect of long-range interactions in the simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods. J Chem Phys 99:8345-8348.
    • (1993) J Chem Phys , vol.99 , pp. 8345-8348
    • York, D.M.1    Darden, T.A.2    Pedersen, L.G.3
  • 99
    • 0030134514 scopus 로고    scopus 로고
    • Chaos in biomolecular dynamics
    • Zhou H, Wang L. 1996. Chaos in biomolecular dynamics. J Phys Chem 100:8101-8105.
    • (1996) J Phys Chem , vol.100 , pp. 8101-8105
    • Zhou, H.1    Wang, L.2


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