메뉴 건너뛰기




Volumn 37, Issue 2, 2003, Pages 240-254

In silico modeling and conformational mobility of DNA duplexes

Author keywords

[No Author keywords available]

Indexed keywords

BIOPOLYMER; DOUBLE STRANDED DNA; DNA; HETERODUPLEX; MESSENGER RNA;

EID: 0037668611     PISSN: 00268984     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review
Times cited : (3)

References (134)
  • 3
    • 33747378396 scopus 로고    scopus 로고
    • Russian source
  • 5
    • 0024278548 scopus 로고
    • The intrinsic curvature of DNA in solution
    • Calladine C.R., Drew H.R., McCall M.J. 1988. The intrinsic curvature of DNA in solution. J. Mol. Biol. 201, 127-137.
    • (1988) J. Mol. Biol. , vol.201 , pp. 127-137
    • Calladine, C.R.1    Drew, H.R.2    McCall, M.J.3
  • 6
  • 7
    • 0028225644 scopus 로고
    • The crystal structure of C-C-A-T-T-A-A-T-G-G: Implications for bending of B-DNA at T-A steps
    • Goodsell D.S., Kaczor-Grzeskowiak M., Dickerson R.E. 1994. The crystal structure of C-C-A-T-T-A-A-T-G-G: implications for bending of B-DNA at T-A steps. J. Mol. Biol. 239, 79-96.
    • (1994) J. Mol. Biol. , vol.239 , pp. 79-96
    • Goodsell, D.S.1    Kaczor-Grzeskowiak, M.2    Dickerson, R.E.3
  • 8
    • 0027318463 scopus 로고
    • Sequence-dependent DNA structure: The role of base stacking interactions
    • Hunter C.A. 1993. Sequence-dependent DNA structure: the role of base stacking interactions. J. Mol. Biol. 230, 1025-1054.
    • (1993) J. Mol. Biol. , vol.230 , pp. 1025-1054
    • Hunter, C.A.1
  • 9
    • 0030003963 scopus 로고    scopus 로고
    • Propeller twisting of base pairs and the conformational mobility of dinucleotide steps in DNA
    • El Hassan M.A., Calladine CR. 1996. Propeller twisting of base pairs and the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol. 259, 95-103.
    • (1996) J. Mol. Biol. , vol.259 , pp. 95-103
    • El Hassan, M.A.1    Calladine, C.R.2
  • 10
    • 0032499635 scopus 로고    scopus 로고
    • The B-DNA dodecamer at high resolution reveals a spine of water on sodium
    • Shiu X., McFail-Isom L., Hu G.G., Williams L.D. 1998. The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry. 37, 8341-8355.
    • (1998) Biochemistry , vol.37 , pp. 8341-8355
    • Shiu, X.1    McFail-Isom, L.2    Hu, G.G.3    Williams, L.D.4
  • 11
    • 0033594498 scopus 로고    scopus 로고
    • A hydrat-ion spine in a B-DNA minor grove
    • Tereshko V., Minasov G., Egli M. 1999. A hydrat-ion spine in a B-DNA minor grove. J. Am. Chem. Soc. 121, 3590-3595.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 3590-3595
    • Tereshko, V.1    Minasov, G.2    Egli, M.3
  • 12
    • 0033600794 scopus 로고    scopus 로고
    • Absence of monovalent cations in the the croslinked dodecamer CGCGAATTCGCG
    • Chiu T.K., Kaczor-Grzekowiak M., Dickerson R.E. 1999. Absence of monovalent cations in the the croslinked dodecamer CGCGAATTCGCG. J. Mol. Biol. 292, 589-608.
    • (1999) J. Mol. Biol. , vol.292 , pp. 589-608
    • Chiu, T.K.1    Kaczor-Grzekowiak, M.2    Dickerson, R.E.3
  • 14
    • 0031423949 scopus 로고    scopus 로고
    • Crystal studies of B-DNA: The answers and the questions
    • Berman H.M. 1997. Crystal studies of B-DNA: the answers and the questions. Biopolymers. 44, 23-44.
    • (1997) Biopolymers , vol.44 , pp. 23-44
    • Berman, H.M.1
  • 15
    • 0029872258 scopus 로고    scopus 로고
    • A useful role for static models in elucidating the behaviour of DNA in solution
    • Calladine C.R., Drew H.R. 1996. A useful role for static models in elucidating the behaviour of DNA in solution. J. Mol. Biol. 257, 479-485.
    • (1996) J. Mol. Biol. , vol.257 , pp. 479-485
    • Calladine, C.R.1    Drew, H.R.2
  • 16
    • 0043203406 scopus 로고    scopus 로고
    • Crystal structures of A-DNA duplexes
    • Wahl M.C., Sundaralingam M. 1997. Crystal structures of A-DNA duplexes. Biopolmers. 44, 45-63.
    • (1997) Biopolmers , vol.44 , pp. 45-63
    • Wahl, M.C.1    Sundaralingam, M.2
  • 17
    • 0033585580 scopus 로고    scopus 로고
    • The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution
    • Tereshko V., Minasov G., Egli M. 1999. The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution. J. Am. Chem. Soc. 121, 470-471.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 470-471
    • Tereshko, V.1    Minasov, G.2    Egli, M.3
  • 18
    • 0032515407 scopus 로고    scopus 로고
    • Sterechemistry of binding of metal cations and water to a phosphate group
    • Schneider B., Kabelae M. 1998. Sterechemistry of binding of metal cations and water to a phosphate group. J. Am. Chem. Soc. 120, 161-165.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 161-165
    • Schneider, B.1    Kabelae, M.2
  • 19
    • 0031755274 scopus 로고    scopus 로고
    • Hydration of the phosphate groups in double-helix DNA
    • Schneider B., Patel K., Berman H.M. 1998. Hydration of the phosphate groups in double-helix DNA. Biophys. J. 75, 2422-2434.
    • (1998) Biophys. J. , vol.75 , pp. 2422-2434
    • Schneider, B.1    Patel, K.2    Berman, H.M.3
  • 20
    • 0034681195 scopus 로고    scopus 로고
    • Sequence specific binding of counter ions to B-DNA
    • Denisov V.P., Halle B. 2000. Sequence specific binding of counter ions to B-DNA. Proc. Natl. Acad. Sci. USA. 97, 629-633.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 629-633
    • Denisov, V.P.1    Halle, B.2
  • 22
    • 0028931709 scopus 로고
    • B-DNA twisting correlated with pair morphology
    • Gorin A.A., Zhurkin V.B., Olson W.K. 1995. B-DNA twisting correlated with pair morphology. J. Mol. Biol. 247, 34-48.
    • (1995) J. Mol. Biol. , vol.247 , pp. 34-48
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 23
    • 0032168436 scopus 로고    scopus 로고
    • Rod models of DNA: Sequence-dependent anisotropic elastic modeling of local bending phenomena
    • Munteanu M.G., Vlahovicek K., Parthasarathy S., Simon I., Pongor S. 1998. Rod models of DNA: sequence-dependent anisotropic elastic modeling of local bending phenomena. TIBS. 23, 341-347.
    • (1998) TIBS , vol.23 , pp. 341-347
    • Munteanu, M.G.1    Vlahovicek, K.2    Parthasarathy, S.3    Simon, I.4    Pongor, S.5
  • 24
    • 0027961109 scopus 로고
    • The influence of salt on the structure and energetics of supercoiled DNA
    • Schlick T., Olson W.K. 1994. The influence of salt on the structure and energetics of supercoiled DNA. Biophys. J. 67, 2146-2166.
    • (1994) Biophys. J. , vol.67 , pp. 2146-2166
    • Schlick, T.1    Olson, W.K.2
  • 25
    • 0028819366 scopus 로고
    • Modulation of intramolecular interctions in superhelical DNA by curved sequences: A Monte Carlo study
    • Klenin K.V., Frank-Kamenetskii M.D., Langovski J. 1995. Modulation of intramolecular interctions in superhelical DNA by curved sequences: a Monte Carlo study. Biophys. J. 68, 81-88.
    • (1995) Biophys. J. , vol.68 , pp. 81-88
    • Klenin, K.V.1    Frank-Kamenetskii, M.D.2    Langovski, J.3
  • 26
    • 0026554929 scopus 로고
    • Supercoiled DNA energetics and dynamics by computer simulation
    • Schlick T., Olson W.K. 1992. Supercoiled DNA energetics and dynamics by computer simulation. J. Mol. Biol. 223, 1089-1119.
    • (1992) J. Mol. Biol. , vol.223 , pp. 1089-1119
    • Schlick, T.1    Olson, W.K.2
  • 27
    • 0030005131 scopus 로고    scopus 로고
    • Simulating DNA at low resolution
    • Olson W. 1996. Simulating DNA at low resolution. Curr. Opin. Struct. Biol. 6, 242-256.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 242-256
    • Olson, W.1
  • 28
    • 0020262664 scopus 로고
    • Computer simulation of DNA double helix dynamics
    • Levit M. 1983. Computer simulation of DNA double helix dynamics. Cold Spring Harbor Symp. Quant. Biol. 47, 251-262.
    • (1983) Cold Spring Harbor Symp. Quant. Biol. , vol.47 , pp. 251-262
    • Levit, M.1
  • 29
    • 0032054952 scopus 로고    scopus 로고
    • Simulations of the molecular dynamics of nucleic acid
    • Auffinger P., Westhof E. 1998. Simulations of the molecular dynamics of nucleic acid. Curr. Opin. Struct. Biol. 8, 227-236.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 227-236
    • Auffinger, P.1    Westhof, E.2
  • 33
    • 0024066560 scopus 로고
    • On the multiple-minima problem in the conformational analysis of polypeptides. An electrostatically driven Monte Carlo method
    • Ripoll D., Scheraga H.A. 1988. On the multiple-minima problem in the conformational analysis of polypeptides. An electrostatically driven Monte Carlo method. Biopolymers. 27, 1283-1303.
    • (1988) Biopolymers , vol.27 , pp. 1283-1303
    • Ripoll, D.1    Scheraga, H.A.2
  • 34
    • 0000666868 scopus 로고    scopus 로고
    • Smart walking: A new methods for Boltzman sampling of protein conformations
    • Zhou R., Berne B.J. 1997. Smart walking: a new methods for Boltzman sampling of protein conformations. J. Chem. Phys. 107, 9185-9196.
    • (1997) J. Chem. Phys. , vol.107 , pp. 9185-9196
    • Zhou, R.1    Berne, B.J.2
  • 35
    • 0032561384 scopus 로고    scopus 로고
    • A glimpse of the holy grail?
    • Berendsen H.J.C. 1998. A glimpse of the holy grail? Science. 282, 642-643.
    • (1998) Science , vol.282 , pp. 642-643
    • Berendsen, H.J.C.1
  • 36
    • 0002625135 scopus 로고    scopus 로고
    • Molecular dynamics simulations: The limit and beyond
    • Eds. Deuflhard P., Hermans J. Berlin: Springer
    • Berendsen H.J.C. 1999. Molecular dynamics simulations: The limit and beyond. In Computational Molecular Dynamics: Challenges, Methods, Ideas. Eds. Deuflhard P., Hermans J. Berlin: Springer, 3-36.
    • (1999) Computational Molecular Dynamics: Challenges, Methods, Ideas , pp. 3-36
    • Berendsen, H.J.C.1
  • 37
    • 33747335525 scopus 로고    scopus 로고
    • URL: 2000. GROMOS96 Home page: http://www.igc.ethz.ch/gromos/; URL: 2002. CHARMM Home Page: http://www.scripps.edu/brooks/charmm_docs/; URL: SIGMA 2002. http://femto.med.unc.edu/SIGMA/index.html; URL: 2001. GROMACS home page, http://www.gromacs.org
    • URL: 2001. AMBER6 Home page: http://www.amber.ucsf.edu/amber/index.html; URL: 2000. GROMOS96 Home page: http://www.igc.ethz.ch/gromos/; URL: 2002. CHARMM Home Page: http://www.scripps.edu/brooks/charmm_docs/; URL: SIGMA 2002. http://femto.med.unc.edu/SIGMA/index.html; URL: 2001. GROMACS home page, http://www.gromacs.org/.
    • (2001)
  • 39
    • 84988053694 scopus 로고
    • An all-atom force fieled for simulation of proteins and nucleic acids
    • Weiner S.J., Kollam P.A., Nguyen D.T., Case D.A. 1986. An all-atom force fieled for simulation of proteins and nucleic acids. J. Comp. Chem. 7, 230-249.
    • (1986) J. Comp. Chem. , vol.7 , pp. 230-249
    • Weiner, S.J.1    Kollam, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 41
    • 33845550595 scopus 로고
    • Energy parameters in polypetides. Upgrating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occuring amino acids
    • Nemethy G., Pottle M.S., Scheraga H.A. 1983. Energy parameters in polypetides. Upgrating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occuring amino acids. J. Phys. Chem. 87, 1883-1901.
    • (1983) J. Phys. Chem. , vol.87 , pp. 1883-1901
    • Nemethy, G.1    Pottle, M.S.2    Scheraga, H.A.3
  • 42
    • 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., Gibbson K.D., Palmer K.A., Yoon C.N., Paterlini G., Zagary A., Ramsey S., Scheraga H.A. 1992. 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, 6472-6489.
    • (1992) J. Phys. Chem. , vol.96 , pp. 6472-6489
    • Nemethy, G.1    Gibbson, K.D.2    Palmer, K.A.3    Yoon, C.N.4    Paterlini, G.5    Zagary, A.6    Ramsey, S.7    Scheraga, H.A.8
  • 43
    • 33645941402 scopus 로고
    • The OPLS potential functions for protein. Energy minimization for crystals of cyclic peptides and crambin
    • Jorgensen W.J., Tirado-Rives J. 1988. The OPLS potential functions for protein. Energy minimization for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110, 16570-1666.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 16570-21666
    • Jorgensen, W.J.1    Tirado-Rives, J.2
  • 44
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen W.L., Maxwell D.S., Tirado-Rives J. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118, 11225-11239.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11239
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 45
    • 0001751804 scopus 로고    scopus 로고
    • Parametrization of aliphatic Clin united atoms of GROMOS96 force field
    • Daura X., Mark A.E., van Gunsteren W.F. 1998. Parametrization of aliphatic Clin united atoms of GROMOS96 force field. J. Comp. Chem. 19, 535-547.
    • (1998) J. Comp. Chem. , vol.19 , pp. 535-547
    • Daura, X.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 46
    • 0037571112 scopus 로고    scopus 로고
    • Merk molecular force field. 1. Basis, form, scope, parametrization and performance of MMFF94
    • Halgren T. A. 1996. Merk molecular force field. 1. Basis, form, scope, parametrization and performance of MMFF94. J. Comp. Chem. 17, 490-519.
    • (1996) J. Comp. Chem. , vol.17 , pp. 490-519
    • Halgren, T.A.1
  • 47
    • 0030021471 scopus 로고    scopus 로고
    • Bio-molecular dynamics comes to age
    • Berendsen H.J.C. 1996. Bio-molecular dynamics comes to age. Science. 271, 954-955.
    • (1996) Science , vol.271 , pp. 954-955
    • Berendsen, H.J.C.1
  • 49
    • 0000795938 scopus 로고
    • Free energies of hydration and pure liquid properties of hydrocarbons from the OPLS all atom model
    • Kaminski G., Duffi E.M., Matsui T., Jorgensen W.L. 1994. Free energies of hydration and pure liquid properties of hydrocarbons from the OPLS all atom model. J. Phys. Chem. 98, 13077-13098.
    • (1994) J. Phys. Chem. , vol.98 , pp. 13077-13098
    • Kaminski, G.1    Duffi, E.M.2    Matsui, T.3    Jorgensen, W.L.4
  • 50
    • 0011134241 scopus 로고    scopus 로고
    • Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
    • Halgren T.A. 1996. Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions. J. Comp. Chem. 17, 520-552.
    • (1996) J. Comp. Chem. , vol.17 , pp. 520-552
    • Halgren, T.A.1
  • 51
    • 0000999989 scopus 로고    scopus 로고
    • Combined Ab Initio/Empirical approach for optimization of Lennard-Jones parameters
    • Yin D., Mackerell A.D.J. 1998. Combined Ab Initio/Empirical approach for optimization of Lennard-Jones parameters. J. Comp. Chem. 18, 334-348.
    • (1998) J. Comp. Chem. , vol.18 , pp. 334-348
    • Yin, D.1    Mackerell, A.D.J.2
  • 52
    • 0001578237 scopus 로고
    • CHARMM92 force field for biomolecular simulations
    • Smith J.C., Karplus M.J. 1994. CHARMM92 force field for biomolecular simulations. J. Am. Chem. Soc. 114, 801-819.
    • (1994) J. Am. Chem. Soc. , vol.114 , pp. 801-819
    • Smith, J.C.1    Karplus, M.J.2
  • 54
    • 0000116495 scopus 로고    scopus 로고
    • Thermodynamic properties of the Williams, OPLS-AA, and MMFF94 all-atom force fields for alkanes
    • Chen B., Marthin M.G., Siepman J.I. 1998. Thermodynamic properties of the Williams, OPLS-AA, and MMFF94 all-atom force fields for alkanes. J. Phys. Chem. B102, 2578-2586.
    • (1998) J. Phys. Chem. , vol.B102 , pp. 2578-2586
    • Chen, B.1    Marthin, M.G.2    Siepman, J.I.3
  • 55
    • 0030745939 scopus 로고    scopus 로고
    • Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assesment of empirial force field
    • Beachy M.D., Chasman D., Murphy R.B., Halgren T.H., Friesner R.A. 1997. Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assesment of empirial force field. J. Am. Chem. Soc. 119, 5908-5920.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 5908-5920
    • Beachy, M.D.1    Chasman, D.2    Murphy, R.B.3    Halgren, T.H.4    Friesner, R.A.5
  • 58
    • 33747333722 scopus 로고    scopus 로고
    • Russian source
  • 59
    • 0343213055 scopus 로고    scopus 로고
    • Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical QM methods (AM1, MNDO/M, PM3), and ab initio HF methods for interaction of DNA bases: Comparision with nonempirical beyond HF results
    • Hobza P., Kabelac M., Sponer J., Mejzlik P., Vondrasek J. 1997. Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical QM methods (AM1, MNDO/M, PM3), and ab initio HF methods for interaction of DNA bases: comparision with nonempirical beyond HF results. J. Comp. Chem. 18, 1137-1150.
    • (1997) J. Comp. Chem. , vol.18 , pp. 1137-1150
    • Hobza, P.1    Kabelac, M.2    Sponer, J.3    Mejzlik, P.4    Vondrasek, J.5
  • 60
    • 0032459726 scopus 로고    scopus 로고
    • Molecular dynamic simulations of environment and sequence dependent DNA conformations: The development of the BMS nucleic acid force field and comparison with experimental results
    • Langley D.R. 1998. Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results. J. Biomol. Struct. Dyn. 16, 487-509.
    • (1998) J. Biomol. Struct. Dyn. , vol.16 , pp. 487-509
    • Langley, D.R.1
  • 61
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
    • Foloppe A., Maccerell A.D. Jr. 2000. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comp. Chem. 21, 86-104.
    • (2000) J. Comp. Chem. , vol.21 , pp. 86-104
    • Foloppe, A.1    Maccerell Jr., A.D.2
  • 62
    • 0000214231 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
    • Foloppe A., Maccerell A.D. Jr. 2000. All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J. Comp. Chem. 21, 104-120.
    • (2000) J. Comp. Chem. , vol.21 , pp. 104-120
    • Foloppe, A.1    Maccerell Jr., A.D.2
  • 63
    • 33747373450 scopus 로고    scopus 로고
    • Russian source
  • 64
    • 33747345529 scopus 로고    scopus 로고
    • Russian source
  • 65
    • 33747366799 scopus 로고    scopus 로고
    • Russian source
  • 66
    • 33747331513 scopus 로고    scopus 로고
    • Russian source
  • 68
    • 0028484011 scopus 로고
    • The spartial structure in liquid water
    • Kusalik P.G., Svishchev I.M. 1994. The spartial structure in liquid water. Science. 265, 1219-1221.
    • (1994) Science , vol.265 , pp. 1219-1221
    • Kusalik, P.G.1    Svishchev, I.M.2
  • 69
    • 0000125216 scopus 로고    scopus 로고
    • Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt M., Hirshberg M., Sharon R., Laiding K.E., Daggett V. 1997. Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution. J. Phys. Chem. B101, 5051-5061.
    • (1997) J. Phys. Chem. , vol.B101 , pp. 5051-5061
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Laiding, K.E.4    Daggett, V.5
  • 70
  • 73
    • 0000035913 scopus 로고    scopus 로고
    • Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximun density
    • Jorgensen W.L., Jenson C. 1998. Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: seeking temperatures of maximun density. J. Comp. Chem. 19, 1179-1186.
    • (1998) J. Comp. Chem. , vol.19 , pp. 1179-1186
    • Jorgensen, W.L.1    Jenson, C.2
  • 74
    • 0000315458 scopus 로고
    • Sensitivity analysis of distribution functions of liquid water
    • Zhu S.-B., Wong C.F. 1993. Sensitivity analysis of distribution functions of liquid water. J. Chem. Phys. 99, 9047-9052.
    • (1993) J. Chem. Phys. , vol.99 , pp. 9047-9052
    • Zhu, S.-B.1    Wong, C.F.2
  • 77
    • 0000042113 scopus 로고
    • Ion solvation in polarizable water: Molecular dynamics simulations
    • Dang L.X., Rice J.E., Caldwell J., Kollman P.A. 1991. Ion solvation in polarizable water: molecular dynamics simulations. J. Am. Chem. Soc. 113, 2481-2486.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 2481-2486
    • Dang, L.X.1    Rice, J.E.2    Caldwell, J.3    Kollman, P.A.4
  • 78
    • 0000651116 scopus 로고    scopus 로고
    • Molecular dynamics study of water clusters, liquid, and liquid-vapor interface of water with many-body potentials
    • Dang L.X., Chang T.-S. 1997. Molecular dynamics study of water clusters, liquid, and liquid-vapor interface of water with many-body potentials. J. Chem. Phys. 106, 8149-8159.
    • (1997) J. Chem. Phys. , vol.106 , pp. 8149-8159
    • Dang, L.X.1    Chang, T.-S.2
  • 79
    • 0000337544 scopus 로고
    • Effective potentials for liquid water using polarizable and nonpolarizable models
    • Wallqvist A., Berne B.J. 1993. Effective potentials for liquid water using polarizable and nonpolarizable models. J. Phys. Chem. 97, 13841-13851.
    • (1993) J. Phys. Chem. , vol.97 , pp. 13841-13851
    • Wallqvist, A.1    Berne, B.J.2
  • 80
    • 0001475763 scopus 로고
    • Distributed multipole analysis, or how to describe a molecular charge distribution
    • Stone A.J. 1981. Distributed multipole analysis, or how to describe a molecular charge distribution. Chem. Phys. Lett. 83, 233-237.
    • (1981) Chem. Phys. Lett. , vol.83 , pp. 233-237
    • Stone, A.J.1
  • 81
    • 84943840245 scopus 로고
    • Towards an accurate intermolecular potential for water
    • Millot C., Stone A.J. 1992. Towards an accurate intermolecular potential for water. Mol. Phys. 77, 439-462.
    • (1992) Mol. Phys. , vol.77 , pp. 439-462
    • Millot, C.1    Stone, A.J.2
  • 82
    • 84947640036 scopus 로고
    • Distributed multipole analysis methods and applications
    • Stone A.J., Alderton M. 1985. Distributed multipole analysis methods and applications. Mol. Phys. 56, 1047-1064.
    • (1985) Mol. Phys. , vol.56 , pp. 1047-1064
    • Stone, A.J.1    Alderton, M.2
  • 83
    • 33846823909 scopus 로고
    • Particle meash Ewald: An N log(N) method for Ewald sums in large systems
    • Darden T., York D., Pedersen L. 1993. Particle meash Ewald: an N log(N) method for Ewald sums in large systems. J. Phys. Chem. 98, 10089-10092.
    • (1993) J. Phys. Chem. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 84
    • 0002997010 scopus 로고
    • A comparision of particle-particle and particle meash and Ewald methods for calculating interactions in periodic molecular systems
    • Lutty B.A., Davis M.E., Tironi I.G., Van Gunsteren W.F. 1994. A comparision of particle-particle and particle meash and Ewald methods for calculating interactions in periodic molecular systems. Mol. Simul. 14, 11-20.
    • (1994) Mol. Simul. , vol.14 , pp. 11-20
    • Lutty, B.A.1    Davis, M.E.2    Tironi, I.G.3    Van Gunsteren, W.F.4
  • 86
    • 0029110156 scopus 로고
    • Toward the accurate modeling of DNA: The importance of long-range electrostatics
    • York D.M., Yang W., Lee H., Darden T., Pedersen L.G. 1995. Toward the accurate modeling of DNA: the importance of long-range electrostatics. J. Am. Chem. Soc. USA. 117, 5000-5002.
    • (1995) J. Am. Chem. Soc. USA , vol.117 , pp. 5000-5002
    • York, D.M.1    Yang, W.2    Lee, H.3    Darden, T.4    Pedersen, L.G.5
  • 88
    • 0000952715 scopus 로고    scopus 로고
    • Effect of periodic box size on aqueous molecular dynamics simulation of DNA dodecamer with particle-meash Ewald method
    • Souza O.N., Ornstein R. 1997. Effect of periodic box size on aqueous molecular dynamics simulation of DNA dodecamer with particle-meash Ewald method. Biophys. J. 72, 2395-2397.
    • (1997) Biophys. J. , vol.72 , pp. 2395-2397
    • Souza, O.N.1    Ornstein, R.2
  • 89
    • 0031566427 scopus 로고    scopus 로고
    • RNA hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(asp) anicodon hairpin
    • Auffinger P., Westhof E. 1997. RNA hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(asp) anicodon hairpin. J. Mol. Biol. 269, 326-341.
    • (1997) J. Mol. Biol. , vol.269 , pp. 326-341
    • Auffinger, P.1    Westhof, E.2
  • 90
    • 0029170114 scopus 로고
    • Molecular dynamics simulations on solvated biomolecular systems: The particle meash Ewald method leads to stable trajectories of DNA, RNA, and proteins
    • Cheatham T.E., Miller J.K., Fox T., Darden T.A., Kollman P.A. 1995. Molecular dynamics simulations on solvated biomolecular systems: the particle meash Ewald method leads to stable trajectories of DNA, RNA, and proteins. J. Am. Chem. Soc. USA. 117, 4193-4194.
    • (1995) J. Am. Chem. Soc. USA , vol.117 , pp. 4193-4194
    • Cheatham, T.E.1    Miller, J.K.2    Fox, T.3    Darden, T.A.4    Kollman, P.A.5
  • 91
    • 0031834850 scopus 로고    scopus 로고
    • Importance of explicit ions for protein stability
    • Ibragimova G.T., Wade R.C. 1998. Importance of explicit ions for protein stability. Biophys. J. 74, 2906-2911.
    • (1998) Biophys. J. , vol.74 , pp. 2906-2911
    • Ibragimova, G.T.1    Wade, R.C.2
  • 92
    • 0038683517 scopus 로고    scopus 로고
    • Ewald artifacts in computer simulstions of ionic solvation and ion-ion interaction: A continuum electrostatic study
    • Hunenberger P.H., McCammon J.A. 1999. Ewald artifacts in computer simulstions of ionic solvation and ion-ion interaction: a continuum electrostatic study. J. Chem. Phys. 110, 1858-1872.
    • (1999) J. Chem. Phys. , vol.110 , pp. 1858-1872
    • Hunenberger, P.H.1    McCammon, J.A.2
  • 93
    • 0037627173 scopus 로고    scopus 로고
    • Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatic study
    • Hunenberger P.H., McCammon J.A. 1999. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatic study. Biophys. Chem. 78, 69-88.
    • (1999) Biophys. Chem. , vol.78 , pp. 69-88
    • Hunenberger, P.H.1    McCammon, J.A.2
  • 94
    • 36449001478 scopus 로고
    • Molecular dynamics algorithm for multiple time scales: System with long range forces
    • Tuckerman M.E., Berne B.J., Rossi A. 1991. Molecular dynamics algorithm for multiple time scales: system with long range forces. J. Chem. Phys. 97, 6811-6815.
    • (1991) J. Chem. Phys. , vol.97 , pp. 6811-6815
    • Tuckerman, M.E.1    Berne, B.J.2    Rossi, A.3
  • 95
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • Tuckerman M.E., Berne B.J., Rossi A. 1992. Reversible multiple time scale molecular dynamics. J. Chem. Phys. 97, 1990-2001.
    • (1992) J. Chem. Phys. , vol.97 , pp. 1990-2001
    • Tuckerman, M.E.1    Berne, B.J.2    Rossi, A.3
  • 96
    • 0000695661 scopus 로고    scopus 로고
    • Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they?
    • Grubmuller H., Tavan P. 1998. Multiple time step algorithms for molecular dynamics simulations of proteins: how good are they? J. Comp. Chem. 19, 1534-1552.
    • (1998) J. Comp. Chem. , vol.19 , pp. 1534-1552
    • Grubmuller, H.1    Tavan, P.2
  • 97
    • 0003085194 scopus 로고
    • Canonical numerical methods for molecular dynamic simulations
    • Okonbor D.I., Skeel R.D. 1994. Canonical numerical methods for molecular dynamic simulations. J. Comp. Chem. 15, 72-79.
    • (1994) J. Comp. Chem. , vol.15 , pp. 72-79
    • Okonbor, D.I.1    Skeel, R.D.2
  • 98
    • 24844474730 scopus 로고    scopus 로고
    • A very fast molecular dynamics method to simulate biomolecular systems with electrostatic interactions
    • Procacci P., Darden T., Marchi M. 1996. A very fast molecular dynamics method to simulate biomolecular systems with electrostatic interactions. J. Phys. Chem. 100, 10464-10468.
    • (1996) J. Phys. Chem. , vol.100 , pp. 10464-10468
    • Procacci, P.1    Darden, T.2    Marchi, M.3
  • 99
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamic simulations with explicit solvent, and an implicit solvent continuum model
    • Vorobjev Y.N., Almagro J.C., Hermans J. 1998. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamic simulations with explicit solvent, and an implicit solvent continuum model. Proteins: Struct. Func. Gen. 32, 399-413.
    • (1998) Proteins: Struct. Func. Gen. , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 100
    • 0033003955 scopus 로고    scopus 로고
    • ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit continuum model
    • Vorobjev Y.N., Hermans J. 1999. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit continuum model. Biophys. Chem. 78, 195-205.
    • (1999) Biophys. Chem. , vol.78 , pp. 195-205
    • Vorobjev, Y.N.1    Hermans, J.2
  • 101
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff D., Sharp K.A., Honig B. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98, 1978-1988.
    • (1994) J. Phys. Chem. , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 102
    • 0000043930 scopus 로고    scopus 로고
    • Solvation free energy of biomacromolecules: Parameters for a modified generalized bom model consistent with the AMBER force field
    • Jayaram B., Sprous D., Beveridge D.L. 1998. Solvation free energy of biomacromolecules: parameters for a modified generalized bom model consistent with the AMBER force field. J. Phys. Chem. 102, 9571-9576.
    • (1998) J. Phys. Chem. , vol.102 , pp. 9571-9576
    • Jayaram, B.1    Sprous, D.2    Beveridge, D.L.3
  • 103
    • 0001246294 scopus 로고    scopus 로고
    • Generalized Born model based on a surface integral formulation
    • Ghosh A., Rapp C.S., Friesner R.A. 1998. Generalized Born model based on a surface integral formulation. J. Phys. Chem. B102, 10983-10990.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 10983-10990
    • Ghosh, A.1    Rapp, C.S.2    Friesner, R.A.3
  • 104
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate DNA helices
    • Srinivasan J., Cheatham T.E. III, Cieplak P., Kollman P.A., Case D.A. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate DNA helices. J. Am. Chem. Soc. 120, 9401-9409.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham III, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 105
    • 0035186285 scopus 로고    scopus 로고
    • Free energy of protein decoys provide insight into determinants of protein stability
    • Vorobjev Y.N., Hermans J. 2001. Free energy of protein decoys provide insight into determinants of protein stability. Protein Sci. 10, 2498-2506.
    • (2001) Protein Sci. , vol.10 , pp. 2498-2506
    • Vorobjev, Y.N.1    Hermans, J.2
  • 106
    • 0031788539 scopus 로고    scopus 로고
    • Molecular dynamic and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution
    • Cheatham T.E. III, Srinivasan J., Case D., Kollman P.A. 1999. Molecular dynamic and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J. Biomol. Struct. Dyn. 16, 265-280.
    • (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 265-280
    • Cheatham III, T.E.1    Srinivasan, J.2    Case, D.3    Kollman, P.A.4
  • 107
    • 0032556243 scopus 로고    scopus 로고
    • Free energy analysis of the conformational preferences of a and B forms of DNA in solution
    • Jayaram B., Sprous D., Young M.A., Beveridge D.L. 1998. Free energy analysis of the conformational preferences of A and B forms of DNA in solution. J. Am. Chem. Soc. 120, 10629-10633.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 10629-10633
    • Jayaram, B.1    Sprous, D.2    Young, M.A.3    Beveridge, D.L.4
  • 108
    • 0001101548 scopus 로고    scopus 로고
    • Free energy analysis of protein-DNA binding: The EcoRI Endonuclease-DNA complex
    • Jayaram B., McConnell K.J., Dixit S.B., Beveridge DL. 1999. Free energy analysis of protein-DNA binding: the EcoRI Endonuclease-DNA complex. J. Comp. Phys. 151, 333-357.
    • (1999) J. Comp. Phys. , vol.151 , pp. 333-357
    • Jayaram, B.1    McConnell, K.J.2    Dixit, S.B.3    Beveridge, D.L.4
  • 109
    • 0033468737 scopus 로고    scopus 로고
    • Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects
    • Srinivasan J., Trevathan M.W., Beroza P., Case D.A. 1999. Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects. Theor. Chem. Acc. 101, 426-434.
    • (1999) Theor. Chem. Acc. , vol.101 , pp. 426-434
    • Srinivasan, J.1    Trevathan, M.W.2    Beroza, P.3    Case, D.A.4
  • 110
  • 111
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for protein in solution
    • Lazaridis T., Karplus M. 1999. Effective energy function for protein in solution. Proteins: Struct. Func. Gen. 35, 133-152.
    • (1999) Proteins: Struct. Func. Gen. , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 112
    • 0037080244 scopus 로고    scopus 로고
    • Rapid grid-based construction of the molecular surface and use of induced surface charge to calculate reaction field energies
    • Rocchia W., Sridharan S., Nicholls A., Alexov E., Chiabrera A., Honig B. 2002. Rapid grid-based construction of the molecular surface and use of induced surface charge to calculate reaction field energies. J. Comp. Chem. 23, 128-137.
    • (2002) J. Comp. Chem. , vol.23 , pp. 128-137
    • Rocchia, W.1    Sridharan, S.2    Nicholls, A.3    Alexov, E.4    Chiabrera, A.5    Honig, B.6
  • 116
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks B.R., Janezic D., Karplus M. 1995. Harmonic analysis of large systems. I. Methodology. J. Comp. Chem. 16, 1522-1542.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 117
    • 84986469420 scopus 로고
    • Harmonic analysis of large systems. II. Comparison of different protein models
    • Janezic D., Brooks B.R. 1995. Harmonic analysis of large systems. II. Comparison of different protein models. J. Comp. Chem. 16, 1543-1553.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1543-1553
    • Janezic, D.1    Brooks, B.R.2
  • 118
    • 84986473952 scopus 로고
    • Harmonic analysis of large systems. III. Comparison with molecular dynamics
    • Janezic D., Venable R.M., Brooks B.R. 1995. Harmonic analysis of large systems. III. Comparison with molecular dynamics. J. Comp. Chem. 16, 1554-1566.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1554-1566
    • Janezic, D.1    Venable, R.M.2    Brooks, B.R.3
  • 120
    • 0030862276 scopus 로고    scopus 로고
    • A 5-nanosecond molecular dynamics trajectory for B-DNA: Analysis of structure, motions and solvation
    • Young M.A., Ravishanker G., Beveridge D.L. 1997. A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions and solvation. Biophys. J. 73, 2313-2336.
    • (1997) Biophys. J. , vol.73 , pp. 2313-2336
    • Young, M.A.1    Ravishanker, G.2    Beveridge, D.L.3
  • 121
    • 0000216904 scopus 로고    scopus 로고
    • Local dielectric environment of B-DNA in solution: Results from a 14 nanosecond molecular dynamics trajectory
    • Young M.A., Jayaram B., Beveridge D.L. 1998. Local dielectric environment of B-DNA in solution: results from a 14 nanosecond molecular dynamics trajectory. J. Phys. Chem. B102, 7666-7669.
    • (1998) J. Phys. Chem. , vol.B102 , pp. 7666-7669
    • Young, M.A.1    Jayaram, B.2    Beveridge, D.L.3
  • 122
    • 0000115258 scopus 로고    scopus 로고
    • Molecular dynamics studies of the conformational preferences of a DNA double helix in water and in an ethanol/water mixture: Theoretical considerations of the A/B transition
    • Sprous D., Young M.A., Beveridge D.L. 1998. Molecular dynamics studies of the conformational preferences of a DNA double helix in water and in an ethanol/water mixture: theoretical considerations of the A/B transition. J. Phys. Chem. 102, 4658-4667.
    • (1998) J. Phys. Chem. , vol.102 , pp. 4658-4667
    • Sprous, D.1    Young, M.A.2    Beveridge, D.L.3
  • 124
    • 0029006896 scopus 로고
    • Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes
    • Young M.A., Ravishanker G., Beveridge D.L., Berman H.M. 1995. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophys. J. 68, 2454-2468.
    • (1995) Biophys. J. , vol.68 , pp. 2454-2468
    • Young, M.A.1    Ravishanker, G.2    Beveridge, D.L.3    Berman, H.M.4
  • 125
    • 0028850111 scopus 로고
    • Structure determination and analysis of local bending in an A-tract DNA duplex: Comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG)
    • Young M.A., Srinivasan J., Goljer I., Kumar S., Beveridge D.L., Bolton P.H. 1995. Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG). Meth. Enzymology. 261, 121-144.
    • (1995) Meth. Enzymology , vol.261 , pp. 121-144
    • Young, M.A.1    Srinivasan, J.2    Goljer, I.3    Kumar, S.4    Beveridge, D.L.5    Bolton, P.H.6
  • 127
    • 0032922174 scopus 로고    scopus 로고
    • A modified version of the force field with improved sugar pucker phases and helical repeat
    • Cheatham T.E. III, Cieplak P., Kollman P.A. 1999. A modified version of the force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16, 845-862.
    • (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 845-862
    • Cheatham III, T.E.1    Cieplak, P.2    Kollman, P.A.3
  • 128
    • 0034682870 scopus 로고    scopus 로고
    • A-tract bending: Insights into experimental structures by computational models
    • Strahs D., Schlick T. 2000. A-tract bending: insights into experimental structures by computational models. J. Mol. Biol. 301, 643-663.
    • (2000) J. Mol. Biol. , vol.301 , pp. 643-663
    • Strahs, D.1    Schlick, T.2
  • 130
    • 0029911794 scopus 로고    scopus 로고
    • Asp: Structuring effects of C-H O hydrogen bonds and of long-range hydration forces
    • Asp: structuring effects of C-H O hydrogen bonds and of long-range hydration forces. J. Am. Chem. Soc. 118, 1181-1189.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 1181-1189
    • Auffinger, P.1    Louise-May, S.2    Westhof, E.3
  • 131
    • 0029776466 scopus 로고    scopus 로고
    • Asp anticodon hairpin: 3 ns of multiple molecular dynamics simulations
    • 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
  • 132
    • 0030723027 scopus 로고    scopus 로고
    • Rules governing the orientation of the 2́ hydroxyl groupi RNA
    • Auffinger P., Westhof E. 1997. Rules governing the orientation of the 2́ hydroxyl groupi RNA. J. Mol. Biol. 274, 54-63.
    • (1997) J. Mol. Biol. , vol.274 , pp. 54-63
    • Auffinger, P.1    Westhof, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.