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.
    190 citations (WOS 246)

  • 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.
    143 citations (WOS 181)

  • Hobza, J. Šponer, T. Reschel: Density functional theory and molecular clusters. Journal of Computational Chemistry 16, 1995, 1315-1325.
    385 citations (WOS 411)

  • 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.
    277 citations (WOS 374)

  • 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.
    272 citations (WOS 352)

  • J. Sponer, P. Hobza: DNA base amino groups and their role in molecular interactions: ab initio and preliminary density functional theory calculations. International Journal of Quantum Chemistry, 57, 1996, 959-970 2
    118 citations (WOS 144)

  • 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
    166 citations (WOS 188)

  • 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.
    157 citations (WOS 207)

  • 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.
    185 citations (WOS 232)

  • J. Šponer, P. Hobza: MP2 and CCSD(T) study on hydrogen bonding, aromatic stacking and nonaromatic stacking. Chemical Physics Letters 267, 1997, 263-270.
    122 citations (WOS 143)

  • J. Sponer, H.A. Gabb, J. Leszczynski, P. Hobza: Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA. A quantum-chemical study. Biophysical Journal 73, 1997, 76-87.
    117 citations (WOS 164)

  • 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.
    164 citations (WOS 193)

  • 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.
    109 citations (WOS 150)

  • N. Spackova, I. Berger, J. Sponer: Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex molecules. Journal of the American Chemical Society 121, 1999, 5519-5534
    103 citations (WOS 133)

  • P. Hobza, J. Šponer: Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chemical Reviews 99, 1999, 3247-3276.
    830 citations (WOS 903)

  • Florian, J. Sponer, A. Warshel: Thermodynamic parameters for stacking and hydrogen bonding of nucleic acid bases in aqueous solution: ab initio/Langevine dipole study. Journal of Physical Chemistry B 103, 1999, 884-892
    101 citations (WOS 137)

  • J. Sponer, J. Leszczynski, P. Hobza: Hydrogen bonding, stacking and cation binding of DNA bases Journal of Molecular Structure (THEOCHEM) 573, 2001, 43-53
    101 citations (WOS 131)

  • J. Šponer, J. Leszczynski, P. Hobza: Electronic properties, hydrogen bonding, stacking and cation-binding of DNA and RNA bases. Biopolymers 61, 2001, 3-36.
    256 citations (WOS 339)

  • 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.
    233 citations (WOS 247)

  • Trygubenko SA, Bogdan TV, Rueda M, Orozco M, Luque FJ, Sponer J, Slavicek P, Hobza P: Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution - Part 1. Cytosine. Physical Chemistry Chemical Physics 4, 2002, 4192-4203.
    132 citations (WOS 141)

  • 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.
    285 citations (WOS 320)

  • F. Lankaš, J. Šponer, J. Langowski, T.E. Cheatham III: DNA base-pair step deformability inferred from molecular dynamics simulations. Biophysical Journal 85, 2003, 2872-2883.
    135 citations (WOS 157)

  • 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.
    310 citations (WOS 347)

  • J. Šponer, P. Jurečka, I. Marchan, F. J. Luque, M. Orozco, P. Hobza: Nature of base stacking. Reference quantum chemical stacking energies in ten unique B-DNA base pair steps. Chemistry - A European Journal 12, 2006, 2854-2865.
    146 citations (WOS 176)

  • 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.
    1,088 citations (WOS 1,161)

  • 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
    961 citations (WOS 1,092)

  • J. Šponer, K. E. Riley, P. Hobza: Nature and magnitude of aromatic stacking of nucleic acid bases. Physical Chemistry Chemical Physics 10, 2008, 2595-2610.
    208 citations (WOS 230)

  • P. Banáš, D. Hollas, M. Zgarbová, P. Jurečka, M. Orozco, T.E, Cheatham, III, J. Šponer, M. Otyepka: Performance of molecular mechanics force fields for RNA simulations. Stability of UUCG and GNRA hairpins. Journal of Chemical Theory and Computation, 6, 2010, 3836-3849.
    120 citations (WOS 166)

  • R. Lavery, K. Zakrzewska, D.L. Beveridge, T.C. Bishop, D.A. Case, T.E. Cheatham, III, S. Dixit, B. Jayaram, F. Lankaš, C. Laughton, J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Špačková, J. Šponer: A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Research 38, 2010, 299-313.
    123 citations (WOS 176)

  • M. Zgarbová, M. Otyepka, J. Šponer, A. Mládek, P. Banáš, T.E. Cheatham, III, P. Jurečka: Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. Journal of Chemical Theory and Computation 7, 2011, 2886-2902
    170 citations (WOS 238)