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Jiří Šponer

Jiří Šponer

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Chemistry
Czechia
2026
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Molecular Biology
Czechia
2026

D-Index & Metrics

Chemistry

D-Index
100
Citations
40956
World Ranking
1258
National Ranking
5

Molecular Biology

D-Index
99
Citations
40215
World Ranking
548
National Ranking
1

Research.com Recognitions

  • 2026 - Research.com Chemistry in Czechia Leader Award
  • 2026 - Research.com Molecular Biology in Czechia Leader Award
  • 2025 - Research.com Chemistry in Czechia Leader Award
  • 2023 - Research.com Chemistry in Czechia Leader Award
  • 2022 - Research.com Chemistry in Czechia Leader Award

Overview

Jiří Šponer is affiliated with Masaryk University in the Czech Republic and has a substantial body of research primarily in biochemistry, genetics, and molecular biology. Their work encompasses both broad and specialized topics within the molecular life sciences.

The scientist's research mainly focuses on molecular biology, covering a total of 232 publications in this subfield. Additional areas of interest include materials chemistry, astronomy and astrophysics, atomic and molecular physics and optics, and ecology.

The primary topics addressed in their work include:

  • DNA and nucleic acid chemistry
  • RNA and protein synthesis mechanisms
  • Advanced biosensing and bioanalysis techniques
  • RNA modifications and cancer
  • RNA research and splicing
  • Bacteriophages and microbial interactions
  • Origins and evolution of life

Jiří Šponer has contributed frequently to several scientific journals and publication venues, particularly:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Journal of Chemical Theory and Computation
  • The Cambridge Structural Database
  • Journal of Chemical Information and Modeling
  • Nucleic Acids Research

Their recent notable publications include:

  • "Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER" (2021), Journal of Chemical Theory and Computation
  • "Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications" (2022), Journal of Chemical Theory and Computation
  • "Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing" (2021), Nature Communications
  • "Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides" (2020), Journal of Chemical Theory and Computation
  • "UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations" (2020), Journal of Chemical Theory and Computation

Jiří Šponer collaborates regularly with a group of frequent co-authors, including Miroslav Krepl, Vojtěch Mlýnský, Judit E. Šponer, Petr Stadlbauer, and Michal Otyepka, reflecting a sustained research network and interdisciplinary exchange.

Best Publications

  • Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers

    Alberto Pérez;Iván Marchán;Daniel Svozil;Daniel Svozil;Jiri Sponer;Jiri Sponer

  • 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.

    Petr Jurečka;Jiří Šponer;Jiří Černý;Pavel Hobza

  • Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations.

    Pavel Hobza;Jiří Šponer

  • Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

    Marie Zgarbová;Michal Otyepka;Michal Otyepka;Jiří Šponer;Jiří Šponer;Arnošt Mládek

  • Promoting transparency and reproducibility in enhanced molecular simulations

    M. Bonomi;M. Bonomi;B. Giovanni;C. Camilloni;G.A. Tribello

  • Density functional theory and molecular clusters

    Pavel Hobza;Jiří šponer;Tomáš Reschel

  • Accurate interaction energies of hydrogen-bonded nucleic acid base pairs.

    Jirí Sponer;Petr Jurecka;Pavel Hobza

  • Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases.

    Jiří Šponer;Jiří Šponer;Jerzy Leszczynski;Pavel Hobza

  • RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

    Jiří Šponer;Giovanni Bussi;Miroslav Krepl;Miroslav Krepl;Pavel Banáš

  • Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

    Marie Zgarbová;Jiří Šponer;Jiří Šponer;Michal Otyepka;Thomas E. Cheatham

  • Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations.

    Pavel Hobza;Jiri Sponer

  • Assessing the Current State of Amber Force Field Modifications for DNA

    Rodrigo Galindo-Murillo;James C. Robertson;Marie Zgarbová;Jiří Šponer;Jiří Šponer

  • Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs

    Jiří Šponer;and Jerzy Leszczyński;Pavel Hobza

  • Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation

    Jiří Šponer;and Jerzy Leszczynski;Pavel Hobza

  • Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

    Pavel Banáš;Daniel Hollas;Marie Zgarbová;Petr Jurečka

  • 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

    David Reha;Martin Kabelac;Filip Ryjacek;Jiri Sponer

  • Nature and magnitude of aromatic stacking of nucleic acid bases

    Jiří Šponer;Kevin E. Riley;Pavel Hobza

  • 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

    Pavel Hobza;Martin Kabeláč;Jiří Šponer;Petr Mejzlík

  • A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

    Richard Lavery;Krystyna Zakrzewska;David Beveridge;Thomas C. Bishop

  • Nonplanar geometries of DNA bases. Ab initio second-order Moeller-Plesset study

    Jiri Sponer;Pavel Hobza

Frequent Co-Authors

Michal Otyepka
Michal Otyepka Palacký University, Olomouc
Pavel Banáš
Pavel Banáš Palacký University, Olomouc
Pavel Hobza
Pavel Hobza Czech Academy of Sciences
Petr Jurečka
Petr Jurečka Palacký University, Olomouc
Jerzy Leszczynski
Jerzy Leszczynski Jackson State University
Jaroslav Koča
Jaroslav Koča Central European Institute of Technology
Thomas E. Cheatham
Thomas E. Cheatham University of Utah
Nils G. Walter
Nils G. Walter University of Michigan–Ann Arbor
Neocles B. Leontis
Neocles B. Leontis Bowling Green State University
Raffaele Saladino
Raffaele Saladino Tuscia University

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