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ORCIDJirí Sponer
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2020 – today
- 2024
[j16]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): 3896-3911 (2024)- [j15]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): 5356 (2024) - 2023
- [j14]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): 2133-2146 (2023) - [j13]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): 2794-2809 (2023) - [j12]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): 4716-4731 (2023) - 2022
- [j11]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): 1012 (2022) - [j10]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): 6182-6200 (2022) - 2021
- [j9]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): 5644-5657 (2021)
2010 – 2019
- 2019
- [j8]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): 3605-3608 (2019) - 2018
- [j7]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) - 2017
- [j6]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): 275-287 (2017) - 2013
- [j5]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): 5362-5383 (2013)
2000 – 2009
- 2009
- [j4]Zdenek Futera, Julia Klenko, Judit E. Sponer, Jirí Sponer, Jaroslav V. Burda:
Interactions of the "piano-stool" [ruthenium(II) (eta6-arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study. J. Comput. Chem. 30(12): 1758-1770 (2009)
1990 – 1999
- 1997
- [j3]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): 1136-1150 (1997) - 1996
- [j2]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): 841-850 (1996) - 1995
- [j1]Pavel Hobza, Jirí Sponer, Tomas Reschel:
Density Functional Theory and Moleculer Clusters. J. Comput. Chem. 16(11): 1315-1325 (1995)
Coauthor Index
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