Jirí Sponer

19 papers Journal 19
YearRankTypeTitle / Venue / Authors
2026 J jnl
Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge.
J. Chem. Inf. Model.
Andrea Nedelníková, Petr Stadlbauer, Pavel Banás, Jirí Sponer, Michal Otyepka, Petra Kührová, Markéta Paloncýová
2025 J jnl
Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.
J. Comput. Chem.
Michal Janecek, Petra Kührová, Vojtech Mlýnský, Petr Stadlbauer, Michal Otyepka, Giovanni Bussi, Jirí Sponer, Pavel Banás
2025 J jnl
How Binding Site Flexibility Promotes RNA Scanning by TbRGG2 RRM: A Molecular Dynamics Simulation Study.
J. Chem. Inf. Model.
Toon Lemmens, Jirí Sponer, Miroslav Krepl
2024 J jnl
Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes".
J. Chem. Inf. Model.
Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás
2024 J jnl
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations.
J. Chem. Inf. Model.
Zhengyue Zhang, Vojtech Mlýnský, Miroslav Krepl, Jirí Sponer, Petr Stadlbauer
2023 J jnl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.
J. Chem. Inf. Model.
Zhengyue Zhang, Jirí Sponer, Giovanni Bussi, Vojtech Mlýnský, Petr Sulc, Chad R. Simmons, Nicholas Stephanopoulos, Miroslav Krepl
2023 J jnl
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations.
J. Chem. Inf. Model.
Petr Stadlbauer, Vojtech Mlýnský, Miroslav Krepl, Jirí Sponer
2023 J jnl
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.
J. Chem. Inf. Model.
Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás
2022 J jnl
A Computational Quantum-Based Perspective on the Molecular Origins of Life's Building Blocks.
Entropy
Gabriele Amante, Judit E. Sponer, Jirí Sponer, Franz Saija, Giuseppe Cassone
2022 J jnl
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions.
J. Chem. Inf. Model.
Klaudia Mráziková, Holger Kruse, Vojtech Mlýnský, Pascal Auffinger, Jirí Sponer
2021 J jnl
Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids.
J. Chem. Inf. Model.
Klaudia Mráziková, Jirí Sponer, Vojtech Mlýnský, Pascal Auffinger, Holger Kruse
2019 J jnl
Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis".
J. Chem. Inf. Model.
Holger Kruse, Jirí Sponer, Pascal Auffinger
2018 J jnl
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.
PLoS Comput. Biol.
Anna Bochicchio, Miroslav Krepl, Fan Yang, Gabriele Varani, Jirí Sponer, Paolo Carloni
2017 J jnl
Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.
J. Chem. Inf. Model.
Marie Zgarbová, Petr Jurecka, Filip Lankas, Thomas E. Cheatham III, Jirí Sponer, Michal Otyepka
2013 J jnl
Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′, 5′-Cyclic GMP.
Entropy
Samanta Pino, Giovanna Costanzo, Alessandra Giorgi, Jirí Sponer, Judit E. Sponer, Ernesto Di Mauro
2009 J jnl
Interactions of the "piano-stool" [ruthenium(II) (eta
J. Comput. Chem.
Zdenek Futera, Julia Klenko, Judit E. Sponer, Jirí Sponer, Jaroslav V. Burda
1997 J jnl
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.
J. Comput. Chem.
Pavel Hobza, Martin Kabelác, Jirí Sponer, Petr Mejzlík, Jirí Vondrásek
1996 J jnl
Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations.
J. Comput. Chem.
Jirí Sponer, Jerzy Leszczynski, Pavel Hobza
1995 J jnl
Density Functional Theory and Moleculer Clusters.
J. Comput. Chem.
Pavel Hobza, Jirí Sponer, Tomas Reschel