Jirí Sponer

Publication Activity (10 Years)

Years Active: 1995-2024
Publications (10 Years): 11

Top Topics

Molecular Dynamics

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás
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. 64 (13) (2024)
Zhengyue Zhang, Vojtech Mlýnský, Miroslav Krepl, Jirí Sponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. J. Chem. Inf. Model. 64 (9) (2024)
Petr Stadlbauer, Vojtech Mlýnský, Miroslav Krepl, Jirí Sponer
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. J. Chem. Inf. Model. 63 (15) (2023)
Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. J. Chem. Inf. Model. 63 (7) (2023)
Zhengyue Zhang, Jirí Sponer, Giovanni Bussi, Vojtech Mlýnský, Petr Sulc, Chad R. Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. J. Chem. Inf. Model. 63 (9) (2023)
Gabriele Amante, Judit E. Sponer, Jirí Sponer, Franz Saija, Giuseppe Cassone
A Computational Quantum-Based Perspective on the Molecular Origins of Life's Building Blocks. Entropy 24 (8) (2022)
Klaudia Mráziková, Holger Kruse, Vojtech Mlýnský, Pascal Auffinger, Jirí Sponer
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. J. Chem. Inf. Model. 62 (23) (2022)
Klaudia Mráziková, Jirí Sponer, Vojtech Mlýnský, Pascal Auffinger, Holger Kruse
Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids. J. Chem. Inf. Model. 61 (11) (2021)
Holger Kruse, Jirí Sponer, Pascal Auffinger
Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis". J. Chem. Inf. Model. 59 (9) (2019)
Anna Bochicchio, Miroslav Krepl, Fan Yang, Gabriele Varani, Jirí Sponer, Paolo Carloni
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. 14 (12) (2018)
Marie Zgarbová, Petr Jurecka, Filip Lankas, Thomas E. Cheatham III, Jirí Sponer, Michal Otyepka
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. 57 (2) (2017)
Samanta Pino, Giovanna Costanzo, Alessandra Giorgi, Jirí Sponer, Judit E. Sponer, Ernesto Di Mauro
Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′, 5′-Cyclic GMP. Entropy 15 (12) (2013)
Zdenek Futera, Julia Klenko, Judit E. Sponer, Jirí Sponer, Jaroslav V. Burda
complexes with water and nucleobases; ab initio and DFT study. J. Comput. Chem. 30 (12) (2009)
Pavel Hobza, Martin Kabelác, Jirí Sponer, Petr Mejzlík, Jirí Vondrásek
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. 18 (9) (1997)
Jirí Sponer, Jerzy Leszczynski, Pavel Hobza
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. 17 (7) (1996)
Pavel Hobza, Jirí Sponer, Tomas Reschel
Density Functional Theory and Moleculer Clusters. J. Comput. Chem. 16 (11) (1995)