List of „100+“ cited papers

All forms of autocitations excluded via SCOPUS (Total WOS data in parenthesis, Nov 2019)

  • J. Šponer, P. Hobza: Nonplanar geometries of DNA bases. Second order Moller-Plesset study. Journal of Physical Chemistry 98, 1994, 3161-3164.
    193 citations (WOS 251)

  • 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.
    144 citations (WOS 185)

  • Hobza, J. Šponer, T. Reschel: Density functional theory and molecular clusters. Journal of Computational Chemistry 16, 1995, 1315-1325.
    400 citations (WOS 430)

  • 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.
    293 citations (WOS 387)

  • 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.
    281 citations (WOS 360)

  • 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
    161 citations (WOS 169)

  • 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
    172 citations (WOS 193)

  • 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.
    166 citations (WOS 216)

  • J. Šponer, J. Leszczynski, P. Hobza: Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations. Journal of Computational Chemistry 17, 1996, 841-850.
    102 citations (WOS 132)

  • 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.
    190 citations (WOS 243)

  • 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 149)

  • 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.
    124 citations (WOS 172)

  • 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.
    171 citations (WOS 200)

  • 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.
    115 citations (WOS 154)

  • 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
    105 citations (WOS 140)

  • P. Hobza, J. Šponer: Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chemical Reviews 99, 1999, 3247-3276.
    846 citations (WOS 937)

  • 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
    100 citations (WOS 142)

  • J. Sponer, J. Leszczynski, P. Hobza: Hydrogen bonding, stacking and cation binding of DNA bases Journal of Molecular Structure (THEOCHEM) 573, 2001, 43-53
    103 citations (WOS 133)

  • J. Šponer, J. Leszczynski, P. Hobza: Electronic properties, hydrogen bonding, stacking and cation-binding of DNA and RNA bases. Biopolymers 61, 2001, 3-36.
    312 citations (WOS 366)

  • 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.
    245 citations (WOS 262)

  • 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.
    148 citations (WOS 154)

  • 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.
    299 citations (WOS 337)

  • 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.
    148 citations (WOS 175)

  • 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.
    332 citations (WOS 373)

  • 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.
    152 citations (WOS 185)

  • 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.
    1,206 citations (WOS 1,318)

  • 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
    1,147 citations (WOS 1,316)

  • 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.
    238 citations (WOS 261)

  • 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.
    140 citations (WOS 204)

  • 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.
    135 citations (WOS 220)

  • 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
    262 citations (WOS 350)

  • M. Zgarbová, F. J. Luque, J. Šponer, T. E. Cheatham III, M. Otyepka, P. Jurečka: Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. Journal of Chemical Theory and Computation, 9, 2013, 2339-2354
    104 citations (WOS 137)

Selected recent

  • M. Zgarbová, M.; Šponer, J.; Otyepka, M.; Cheatham, T. E.; Galindo-Murillo, R.; Jurečka, P., Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. Journal of Chemical Theory and Computation 2015, 11, 5723-5736
    84 citations (WOS 95)

  • Galindo-Murillo, R.; Robertson, J. C.; Zgarbova, M.; Sponer, J.; Otyepka, M.; Jurecka, P.; Cheatham, T. E., Assessing the Current State of AMBER Force Field Modifications for DNA. Journal of Chemical Theory and Computation 2016, 12, 4114–4127.
    69 citations (WOS 79)

  • Šponer, J.; Bussi, G.; Krepl, M.; Banáš, P.; Bottaro, S.; Cunha, R. A.; Gil-Ley, A.; Pinamonti, G.; Poblete, S.; Jurečka, P., et al., RNA Structural Dynamics as Captured by Molecular Simulations: A Comprehensive Overview. Chemical Reviews 2018, 118, 4177–4338
    56 citations (WOS 76)