DSDNA

Structure and Dynamics of Nucleic Acids

Citations

All forms of autocitations manually excluded (Total WOS data in parenthesis)

  • J. Šponer, P. Hobza: Nonplanar geometries of DNA bases. Second order Moller-Plesset study. Journal of Physical Chemistry 98, 1994, 3161-3164.
    170 citations (WOS 222)

  • P. Hobza, J. Šponer, M. Polášek: H-bonded and stacked DNA base pairs: cytosine dimer. Ab initio second order Moller-Plesset study. Journal of the American Chemical Society 117, 1995, 792-798.
    130 citations (WOS 159)

  • Hobza, J. Šponer, T. Reschel: Density functional theory and molecular clusters. Journal of Computational Chemistry 16, 1995, 1315-1325.
    258 citations (WOS 300)

  • J. Šponer, J. Leszczynski, P. Hobza: Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation. Journal of Physical Chemistry 100, 1996, 1965-1974.
    259 citations (WOS 334)

  • J. Šponer, J. Leszczynski, P. Hobza: On the nature of nucleic acid base stacking. Nonempirical ab initio and empirical potential characterization of 10 stacked base pairs. Comparison of stacked and H-bonded base pairs. Journal of Physical Chemistry 100, 1996, 5590-5596.
    221 citations (WOS 292)

  • J.V. Burda, J. Šponer, P. Hobza: An ab initio study of the interaction of guanine and adenine with various monovalent and bivalent metal cations (Li+, Na+, K+, Rb+, Cs+, Cu+, Ag+, Au+, Mg2+, Ca2+, Sr2+, Ba2+, Zn2+, Cd2+, and Hg2+). Journal of Physical Chemistry 100, 1996, 7250-7255
    134 citations (WOS 159)

  • J. Šponer, J. Leszczynski, P. Hobza: Hydrogen bonding and stacking of DNA bases. A review of ab initio quantum-chemical studies. Journal of Biomolecular Structure and Dynamics 14, 1996, 117-136.
    133 citations (WOS 180)

  • P. Hobza, M. Kabeláč, J. Šponer, P. Mejzlík, J. Vondrášek: Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3) and ab initio Hartree-Fock method for interaction of DNA bases. Comparison with nonempirical beyond-Hartree-Fock results. Journal of Computational Chemistry 18, 1997, 1136-1150.
    179 citations (WOS 209)

  • J. Šponer, P. Hobza: MP2 and CCSD(T) study on hydrogen bonding, aromatic stacking and nonaromatic stacking. Chemical Physics Letters 267, 1997, 263-270.
    117 citations (WOS 135)

  • J.V. Burda, J. Šponer, J. Leszczynski, P. Hobza: Interaction of DNA base pairs with various metal cations (Mg2+, Ca2+, Sr2+, Ba2+, Zn2+, Cd2+, and Hg2+). Nonempirical ab initio calculations on structures, energies, and nonadditivity of interactions. Journal of Physical Chemistry B 101, 1997, 9670-9677.
    117 citations (WOS 153)

  • J. Šponer, J.V. Burda, M. Sabat, J. Leszczynski, P. Hobza: Interaction between the guanine-cytosine Watson-Crick DNA base pair and hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations. Journal of Physical Chemistry A 102, 1998, 5951-5957.
    100 citations (126 WOS)

  • P. Hobza, J. Šponer: Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chemical Reviews 99, 1999, 3247-3276.
    656 citations (WOS 734)

  • J. Šponer, J. Leszczynski, P. Hobza: Electronic properties, hydrogen bonding, stacking and cation-binding of DNA and RNA bases. Biopolymers 61, 2001, 3-36.
    190 citations (WOS 215)

  • D. Řeha , M. Kabeláč, F. Ryjáček, J. Šponer, J.E. Šponer, M. Elstner; S. Suhai, P. Hobza: Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4 ',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study. Journal of the American Chemical Society 124, 2002, 3366-3376.
    167 citations (WOS 185)

  • P. Hobza, J. Šponer: Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations: Journal of the American Chemical Society. 124, 2002, 11802-11808.96.
    197 citations (WOS 230)

  • J. Šponer, P. Jurečka, P. Hobza: Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. Journal of the American Chemical Society 126, 2004, 10142 - 10151.
    200 citations (WOS 234)

  • P. Jurečka, J. Šponer, J.Černý, P. Hobza: Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Physical Chemistry Chemical Physics 8, 2006, 1985-1993.
    470 citations (WOS 550)

  • A. Pérez, I. Marchán, D. Svozil, J. Šponer, T. E. Cheatham, III, C.A. Laughton, M. Orozco: *Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ  Conformers. Biophysical Journal 2007 92: 3817-3829
    245 citations (WOS 329)

All forms of autocitations manually excluded (Total WOS data in parenthesis)

  • J. Šponer, P. Hobza: Nonplanar geometries of DNA bases. Second order Moller-Plesset study. Journal of Physical Chemistry 98, 1994, 3161-3164.
    168 citations (WOS 220)

  • P. Hobza, J. Šponer, M. Polášek: H-bonded and stacked DNA base pairs: cytosine dimer. Ab initio second order Moller-Plesset study. Journal of the American Chemical Society 117, 1995, 792-798.
    125 citations (WOS 154)

  • Hobza, J. Šponer, T. Reschel: Density functional theory and molecular clusters. Journal of Computational Chemistry 16, 1995, 1315-1325.
    242 citations (WOS 282)

  • J. Šponer, J. Leszczynski, P. Hobza: Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation. Journal of Physical Chemistry 100, 1996, 1965-1974.
    251 citations (WOS 325)

  • J. Šponer, J. Leszczynski, P. Hobza: On the nature of nucleic acid base stacking. Nonempirical ab initio and empirical potential characterization of 10 stacked base pairs. Comparison of stacked and H-bonded base pairs. Journal of Physical Chemistry 100, 1996, 5590-5596.
    213 citations (WOS 281)

  • J.V. Burda, J. Šponer, P. Hobza: An ab initio study of the interaction of guanine and adenine with various monovalent and bivalent metal cations (Li+, Na+, K+, Rb+, Cs+, Cu+, Ag+, Au+, Mg2+, Ca2+, Sr2+, Ba2+, Zn2+, Cd2+, and Hg2+). Journal of Physical Chemistry 100, 1996, 7250-7255
    124 citations (WOS 148)

  • J. Šponer, J. Leszczynski, P. Hobza: Hydrogen bonding and stacking of DNA bases. A review of ab initio quantum-chemical studies. Journal of Biomolecular Structure and Dynamics 14, 1996, 117-136.
    130 citations (WOS 177)

  • P. Hobza, M. Kabeláč, J. Šponer, P. Mejzlík, J. Vondrášek: Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3) and ab initio Hartree-Fock method for interaction of DNA bases. Comparison with nonempirical beyond-Hartree-Fock results. Journal of Computational Chemistry 18, 1997, 1136-1150.
    173 citations (WOS 203)

  • J. Šponer, P. Hobza: MP2 and CCSD(T) study on hydrogen bonding, aromatic stacking and nonaromatic stacking. Chemical Physics Letters 267, 1997, 263-270.
    113 citations (WOS 131)

  • J.V. Burda, J. Šponer, J. Leszczynski, P. Hobza: Interaction of DNA base pairs with various metal cations (Mg2+, Ca2+, Sr2+, Ba2+, Zn2+, Cd2+, and Hg2+). Nonempirical ab initio calculations on structures, energies, and nonadditivity of interactions. Journal of Physical Chemistry B 101, 1997, 9670-9677.
    109 citations (WOS 142)

  • P. Hobza, J. Šponer: Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chemical Reviews 99, 1999, 3247-3276.
    628 citations (WOS 701)

  • J. Šponer, J. Leszczynski, P. Hobza: Electronic properties, hydrogen bonding, stacking and cation-binding of DNA and RNA bases. Biopolymers 61, 2001, 3-36.
    182 citations (WOS 204)

  • D. Řeha , M. Kabeláč, F. Ryjáček, J. Šponer, J.E. Šponer, M. Elstner; S. Suhai, P. Hobza: Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4 ',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study. Journal of the American Chemical Society 124, 2002, 3366-3376.
    157 citations (WOS 173)

  • P. Hobza, J. Šponer: Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations: Journal of the American Chemical Society. 124, 2002, 11802-11808.96.
    186 citations (WOS 215)

  • J. Šponer, P. Jurečka, P. Hobza: Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. Journal of the American Chemical Society 126, 2004, 10142 - 10151.
    185 citations (WOS 214)

  • P. Jurečka, J. Šponer, J.Černý, P. Hobza: Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Physical Chemistry Chemical Physics 8, 2006, 1985-1993.
    387 citations (WOS 444)

  • A. Pérez, I. Marchán, D. Svozil, J. Šponer, T. E. Cheatham, III, C.A. Laughton, M. Orozco: *Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ  Conformers. Biophysical Journal 2007 92: 3817-3829
    196 citations (WOS 237)