Density Functional Theory and Moleculer Clusters. - Pavel Hobza; Jirí Sponer; Tomas Reschel (J. Comput. Chem., 1995)

Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations. - Jirí Sponer; Jerzy Leszczynski; Pavel Hobza (J. Comput. Chem., 1996)

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 Kabelác; Jirí Sponer; Petr Mejzlík; Jirí Vondrásek (J. Comput. Chem., 1997)

Interactions of the "piano-stool" [ruthenium(II) (eta6-arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study. - Zdenek Futera; Julia Klenko; Judit E. Sponer; Jirí Sponer; Jaroslav V. Burda (J. Comput. Chem., 2009)

Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′, 5′-Cyclic GMP. - Samanta Pino; Giovanna Costanzo; Alessandra Giorgi; Jirí Sponer; Judit E. Sponer; Ernesto Di Mauro (Entropy, 2013)

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. - Marie Zgarbová; Petr Jurecka; Filip Lankas; Thomas E. Cheatham III; Jirí Sponer; Michal Otyepka (J. Chem. Inf. Model., 2017)

Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study. - Anna Bochicchio; Miroslav Krepl; Fan Yang; Gabriele Varani; Jirí Sponer; Paolo Carloni (PLoS Comput. Biol., 2018)

Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis". - Holger Kruse; Jirí Sponer; Pascal Auffinger (J. Chem. Inf. Model., 2019)

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids. - Klaudia Mráziková; Jirí Sponer; Vojtech Mlýnský; Pascal Auffinger; Holger Kruse (J. Chem. Inf. Model., 2021)

A Computational Quantum-Based Perspective on the Molecular Origins of Life's Building Blocks. - Gabriele Amante; Judit E. Sponer; Jirí Sponer; Franz Saija; Giuseppe Cassone (Entropy, 2022)

Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. - Klaudia Mráziková; Holger Kruse; Vojtech Mlýnský; Pascal Auffinger; Jirí Sponer (J. Chem. Inf. Model., 2022)

Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. - Petra Kührová; Vojtech Mlýnský; Michal Otyepka; Jirí Sponer; Pavel Banás (J. Chem. Inf. Model., 2023)

Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. - Zhengyue Zhang; Jirí Sponer; Giovanni Bussi; Vojtech Mlýnský; Petr Sulc; Chad R. Simmons; Nicholas Stephanopoulos; Miroslav Krepl (J. Chem. Inf. Model., 2023)

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. - Petr Stadlbauer; Vojtech Mlýnský; Miroslav Krepl; Jirí Sponer (J. Chem. Inf. Model., 2023)

Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes". - Petra Kührová; Vojtech Mlýnský; Michal Otyepka; Jirí Sponer; Pavel Banás (J. Chem. Inf. Model., 2024)

Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. - Zhengyue Zhang; Vojtech Mlýnský; Miroslav Krepl; Jirí Sponer; Petr Stadlbauer (J. Chem. Inf. Model., 2024)

Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space. - Michal Janecek; Petra Kührová; Vojtech Mlýnský; Petr Stadlbauer; Michal Otyepka; Giovanni Bussi; Jirí Sponer; Pavel Banás (J. Comput. Chem., 2025)

How Binding Site Flexibility Promotes RNA Scanning by TbRGG2 RRM: A Molecular Dynamics Simulation Study. - Toon Lemmens; Jirí Sponer; Miroslav Krepl (J. Chem. Inf. Model., 2025)