List of „100+“ cited papers

All forms of autocitations excluded via SCOPUS (Total WOS data in parenthesis, Mar 2025)

• J. Šponer, P. Hobza: Nonplanar geometries of DNA bases. Second order Moller-Plesset study. Journal of Physical Chemistry 98, 1994, 3161-3164.
  200 citations (WOS 256)

• 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.
  146 citations (WOS 186)

• Hobza, J. Šponer, T. Reschel: Density functional theory and molecular clusters. Journal of Computational Chemistry 16, 1995, 1315-1325.
  452 citations (WOS 488)

• 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.
  319 citations (WOS 408)

• J. Šponer, J. Leszczynski, P. Hobza: 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.
  316 citations (WOS 390)

• 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
  209 citations (WOS 215)

• 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
  189 citations (WOS 212)

• 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.
  180 citations (WOS 226)

• 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.
  120 citations (WOS 147)

• 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.
  212 citations (WOS 268)

• J. Šponer, P. Hobza: MP2 and CCSD(T) study on hydrogen bonding, aromatic stacking and nonaromatic stacking. Chemical Physics Letters 267, 1997, 263-270.
  127 citations (WOS 153)

• 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.
  134 citations (WOS 185)

• 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.
  196 citations (WOS 229)

• 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.
  128 citations (WOS 172)

• 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
  125 citations (WOS 159)

• P. Hobza, J. Šponer: Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chemical Reviews 99, 1999, 3247-3276.
  912 citations (WOS 1,003)

• 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
  114 citations (WOS 156)

• P. Hobza, J. Sponer, E. Cubero, M. Orozco, F.J. Luque: C-H...O contacts in the adenine.uracil and uracil...uracil nucleic acid base pairs: Nonempirical ab initio study with inclusion of electron correlation effects. Journal of Physical Chemistry B 104, 2000, 6286-6292

113 citations (WOS 128)

• F. Lankas, J. Sponer, P. Hobza, J. Langowski: Sequence-dependent elastic properties of DNA. Journal of Molecular Biology 299, 2000, 697-712.

116 citations (WOS 137)

• J. Sponer, M. Sabat, L. Gorb, J. Leszczynski, B. Lippert, P. Hobza: The Effect of Metal Binding to the N7 Site of Purine Nucleotides on Their Structure, Energy, and Involvement in Base Pairing Journal of Physical Chemistry B 104, 2000, 7535-7544.

101 citations (WOS 136)

• J. Sponer, J. Leszczynski, P. Hobza: Hydrogen bonding, stacking and cation binding of DNA bases Journal of Molecular Structure (THEOCHEM) 573, 2001, 43-53
  118 citations (WOS 124)

• J. Šponer, J. Leszczynski, P. Hobza: Electronic properties, hydrogen bonding, stacking and cation-binding of DNA and RNA bases. Biopolymers 61, 2001, 3-36.
  359 citations (WOS 409)

• 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.
  283 citations (WOS 296)

• 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.
  169 citations (WOS 178)

• 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.
  337 citations (WOS 376)

• N. Špačková, T. E. Cheatham, III, F. Ryjáček, F. Lankaš, L. van Meervelt, P. Hobza and J. Šponer, Molecular dynamics simulations and thermodynamics analysis of DNA - drug complexes. Minor groove binding between 4?,6-diamidino-2-phenylindole (DAPI) and DNA duplexes in solution. Journal of the American Chemical Society 125, 2003, 1759-1769.

122 citations (WOS 134)

• 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.
  192 citations (WOS 218)

• 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.
  372 citations (WOS 411)

• 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.
  173 citations (WOS 206)

• 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.
  1,562 citations (WOS 1,626)

• 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
  1,692 citations (WOS 1,885)

• 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.
  269 citations (WOS 299)

• 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.
  234 citations (WOS 314)

• 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.
  170 citations (WOS 271)

• 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
  706 citations (WOS 822)

• M. Krepl, M. Zgarbova, P. Stadlbauer, M. Otyepka, P. Banas, J. Koca, T.E. Cheatham, III, P. Jurecka, J. Sponer: Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA Journal of Chemical Theory and Computation, 8, 2012, 2506-2520.

162 citations (WOS 215)

• 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
  184 citations (WOS 240)

• J. Sponer, J. E. Sponer, A. Mladek, P. Jurecka, P. Banas, M. Otyepka: Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment. Biopolymers, 2013, 99, 978-988.

100 citations (WOS 114)

• Zgarbová, M.; Otyepka, M.; Šponer, J.; Lankaš, F.; Jurečka, P., Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA. Journal of Chemical Theory and Computation 2014, 10, 3177-3189.

113 citations (WOS 136)

• Pasi, M.; Maddocks, J. H.; Beveridge, D.; Bishop, T. C.; Case, D. A.; Cheatham, T.; Dans, P. D.; Jayaram, B.; Lankas, F.; Laughton, C.; Mitchell, J.; Osman, R.; Orozco, M.; Pérez, A.; Petkevičiūtė, D.; Spackova, N.; Sponer, J.; Zakrzewska, K.; Lavery, R., μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research 2014, 42, 12272-12283.

105 citations (WOS 166)

• Ferus, M.; Nesvorny, D.; Sponer, J.; Kubelik, P.; Michalcikova, R.; Shestivska, V.; Sponer, J. E.; Civis, S., High-energy chemistry of formamide: A unified mechanism of nucleobase formation. Proceedings of the National Academy of Sciences of the United States of America 2015, 112, 657-662.

112 citations (WOS 145)

• 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.

346 citations (WOS 394)

• 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.
  345 citations (WOS 368)

• Šponer, J.; Bussi, G.; Krepl, M.; Banáš, P.; Bottaro, S.; Cunha, R. A.; Gil-Ley, A.; Pinamonti, G.; Poblete, S.; Jurečka, P.; Walter N.G.; Otyepka, M., RNA Structural Dynamics as Captured by Molecular Simulations: A Comprehensive Overview. Chemical Reviews 2018, 118, 4177–4338
  321 citations (WOS 381)

• PLUMED consortium: Bonomi, M.; Bussi, G.; Camilloni, C.; Tribello, G. A.; Banáš, P.;…. Sponer J.; et al., Promoting Transparency and Reproducibility in Enhanced Molecular Simulations. Nature Methods 2019, 16, 670-673.

432 citations (WOS 711)