Jiřı Šponer (Jiří Šponer, Jiri Sponer)

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 74

Top Topics

Molecular Dynamics

Electron Transfer

Circulating Tumor

Top Venues

Journal of chemical theory and computation

Journal of chemical information and modeling

Nature communications

Angewandte Chemie (International ed. in English)

This page only lists publications with an associated author ORCID identifier.

Publications

Petra Kührová, Vojtěch Mlýnský, Michal Otyepka, Jiřı Šponer, Pavel Banáš
Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes". Journal of chemical information and modeling 64 (13) (2024)
Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling 64 (9) (2024)
Barbora Knappeová, Vojtěch Mlýnský, Martin Pykal, Jiřı Šponer, Pavel Banáš, Michal Otyepka, Miroslav Krepl
Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes. Journal of chemical theory and computation 20 (15) (2024)
Petra Kührová, Vojtěch Mlýnský, Michal Otyepka, Jiřı Šponer, Pavel Banáš
Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes". Journal of chemical information and modeling 64 (13) (2024)
Valerio Piomponi, Miroslav Krepl, Jiřı Šponer, Giovanni Bussi
Molecular Simulations to Investigate the Impact of N6-Methylation in RNA Recognition: Improving Accuracy and Precision of Binding Free Energy Prediction. The journal of physical chemistry. B (2024)
Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling (2024)
Petra Kührová, Vojtěch Mlýnský, Michal Otyepka, Jiřı Šponer, Pavel Banáš
Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes". Journal of chemical information and modeling (2024)
Martin Gajarsky, Petr Stadlbauer, Jiřı Šponer, Anne Cucchiarini, Michaela Dobrovolna, Václav Brázda, Jean-Louis Mergny, Lukas Trantirek, Martina Lenarčič Živković
DNA Quadruplex Structure with a Unique Cation Dependency. Angewandte Chemie (International ed. in English) 63 (7) (2024)
Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling 64 (9) (2024)
Martin Gajarsky, Petr Stadlbauer, Jiřı Šponer, Anne Cucchiarini, Michaela Dobrovolna, Václav Brázda, Jean-Louis Mergny, Lukas Trantirek, Martina Lenarčič Živković
DNA Quadruplex Structure with a Unique Cation Dependency. Angewandte Chemie (International ed. in English) 63 (7) (2024)
Barbora Knappeová, Vojtěch Mlýnský, Martin Pykal, Jiřı Šponer, Pavel Banáš, Michal Otyepka, Miroslav Krepl
Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes. Journal of chemical theory and computation 20 (15) (2024)
Barbora Knappeová, Vojtěch Mlýnský, Martin Pykal, Jiřı Šponer, Pavel Banáš, Michal Otyepka, Miroslav Krepl
Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes. Journal of chemical theory and computation (2024)
Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling 64 (9) (2024)
Barbora Knappeová, Vojtěch Mlýnský, Martin Pykal, Jiřı Šponer, Pavel Banáš, Michal Otyepka, Miroslav Krepl
Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes. Journal of chemical theory and computation 20 (15) (2024)
Martin Gajarsky, Petr Stadlbauer, Jiřı Šponer, Anne Cucchiarini, Michaela Dobrovolna, Václav Brázda, Jean-Louis Mergny, Lukas Trantirek, Martina Lenarčič Živković
DNA Quadruplex Structure with a Unique Cation Dependency. Angewandte Chemie (International ed. in English) 63 (7) (2024)
Giuseppe Cassone, Franz Saija, Jiřı Šponer, Sason S Shaik
The Reactivity-Enhancing Role of Water Clusters in Ammonia Aqueous Solutions. The journal of physical chemistry letters (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling (2023)
Petr Stadlbauer, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. Journal of chemical information and modeling (2023)
Olivia Love, Rodrigo Galindo-Murillo, Marie Zgarbová, Jiřı Šponer, Petr Jurečka, Thomas E Cheatham
Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition. Journal of chemical theory and computation (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Corinna L Kufner, Sarah J Crucilla, Dian Ding, Petr Stadlbauer, Jiřı Šponer, Jack W Szostak, Dimitar D Sasselov, Rafał Szabla
Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern. Chemical science 15 (6) (2023)
Petra Kührová, Vojtěch Mlýnský, Michal Otyepka, Jiřı Šponer, Pavel Banáš
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. Journal of chemical information and modeling (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Martin Gajarsky, Petr Stadlbauer, Jiřı Šponer, Anne Cucchiarini, Michaela Dobrovolna, Václav Brázda, Jean-Louis Mergny, Lukas Trantirek, Martina Lenarčič Živković
DNA Quadruplex Structure with a Unique Cation Dependency. Angewandte Chemie (International ed. in English) (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Vojtěch Mlýnský, Petra Kührová, Petr Stadlbauer, Miroslav Krepl, Michal Otyepka, Pavel Banáš, Jiřı Šponer
Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations. Journal of chemical theory and computation (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Corinna L Kufner, Sarah J Crucilla, Dian Ding, Petr Stadlbauer, Jiřı Šponer, Jack W Szostak, Dimitar D Sasselov, Rafał Szabla
Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern. Chemical science 15 (6) (2023)
Klaudia Mrazikova, Holger Kruse, Vojtěch Mlýnský, Pascal Auffinger, Jiřı Šponer
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. Journal of chemical information and modeling (2022)
Thorben Fröhlking, Vojtěch Mlýnský, Michal Janeček, Petra Kührová, Miroslav Krepl, Pavel Banáš, Jiřı Šponer, Giovanni Bussi
Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field. Journal of chemical theory and computation 18 (7) (2022)
Vojtěch Mlýnský, Michal Janeček, Petra Kührová, Thorben Fröhlking, Michal Otyepka, Giovanni Bussi, Pavel Banáš, Jiřı Šponer
Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications. Journal of chemical theory and computation 18 (4) (2022)
Pavlína Pokorná, Miroslav Krepl, Sébastien Campagne, Jiřı Šponer
Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations. The journal of physical chemistry. B 126 (45) (2022)
Giuseppe Cassone, Jiřı Šponer, Judit E Sponer, Franz Saija
Electrofreezing of Liquid Ammonia. The journal of physical chemistry letters 13 (42) (2022)
Chad R Simmons, Tara MacCulloch, Miroslav Krepl, Michael Matthies, Alex Buchberger, Ilyssa Crawford, Jiřı Šponer, Petr Sulc, Nicholas Stephanopoulos, Hao Yan
The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly. Nature communications 13 (1) (2022)
Daniel G A Smith, Annabelle T Lolinco, Zachary L Glick, Jiyoung Lee, Asem Alenaizan, Taylor A Barnes, Carlos H Borca, Roberto Di Remigio, David L Dotson, Sebastian Ehlert, Alexander G Heide, Michael F Herbst, Jan Hermann, Colton B Hicks, Joshua T Horton, Adrian G Hurtado, Peter Kraus, Holger Kruse, Sebastian J R Lee, Jonathon P Misiewicz, Levi N Naden, Farhad Ramezanghorbani, Maximilian Scheurer, Jeffrey B Schriber, Andrew C Simmonett, Johannes Steinmetzer, Jeffrey R Wagner, Logan Ward, Matthew Welborn, Doaa Altarawy, Jamshed Anwar, John D Chodera, Andreas Dreuw, Heather J Kulik, Fang Liu, Todd J Martinez, Devin A Matthews, Henry F Schaefer, Jiřı Šponer, Justin M Turney, Lee-Ping Wang, Nuwan De Silva, Rollin A King, John F Stanton, Mark S Gordon, Theresa L Windus, C David Sherrill, Lori A Burns
Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. The Journal of chemical physics 155 (20) (2021)
Zhengyue Zhang, Jennifer Vögele, Klaudia Mráziková, Holger Kruse, Xiaohui Cang, Jens Wöhnert, Miroslav Krepl, Jiřı Šponer
Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments. The journal of physical chemistry. B 125 (3) (2021)
Martin Ferus, Giuseppe Cassone, Vladimír Táborský, Alan Heays, Lukáš Petera, Antonín Knížek, Tadeáš Kalvoda, Milan Bousa, Jiřı Šponer, Judit E Šponer, Petr Kubelík, Jan Drápal, Jan Stehlík, Svatopluk Civiš
Thermal Decomposition of Cocaine and Methamphetamine Investigated by Infrared Spectroscopy and Quantum Chemical Simulations. ACS omega 6 (22) (2021)
Mikołaj J Janicki, Corinna L Kufner, Zoe R Todd, Seohyun Chris Kim, Derek K O'Flaherty, Jack W Szostak, Jiřı Šponer, Robert W Góra, Dimitar D Sasselov, Rafał Szabla
Ribose Alters the Photochemical Properties of the Nucleobase in Thionated Nucleosides. The journal of physical chemistry letters 12 (28) (2021)
Klaudia Mrazikova, Jiřı Šponer, Vojtěch 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. Journal of chemical information and modeling 61 (11) (2021)
Miroslav Krepl, Fred Franz Damberger, Christine von Schroetter, Dominik Theler, Pavlína Pokorná, Frédéric H-T Allain, Jiřı Šponer
Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration. The journal of physical chemistry. B 125 (28) (2021)
Antoine Cléry, Miroslav Krepl, Cristina K X Nguyen, Ahmed Moursy, Hadi Jorjani, Maria Katsantoni, Michal Okoniewski, Nitish Mittal, Mihaela Zavolan, Jiřı Šponer, Frédéric Hai-Trieu Allain
Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing. Nature communications 12 (1) (2021)
Rafał Szabla, Magdalena Zdrowowicz, Paulina Spisz, Nicholas J Green, Petr Stadlbauer, Holger Kruse, Jiřı Šponer, Janusz Rak
2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions. Nature communications 12 (1) (2021)
Petr Stadlbauer, Barira Islam, Michal Otyepka, Jielin Chen, David Monchaud, Jun Zhou, Jean-Louis Mergny, Jiřı Šponer
Insights into G-Quadruplex-Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding. Journal of chemical theory and computation 17 (3) (2021)
Sreekar Wunnava, Christina F Dirscherl, Jakub Výravský, Ales Kovařík, Roman Matyášek, Jiřı Šponer, Dieter Braun, Judit E Sponer
Acid-Catalyzed RNA-Oligomerization from 3',5'-cGMP. Chemistry (Weinheim an der Bergstrasse, Germany) (2021)
Marie Zgarbová, Jiřı Šponer, Petr Jurečka
Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER. Journal of chemical theory and computation 17 (10) (2021)
Michal Janeček, Petra Kührová, Vojtěch Mlýnský, Michal Otyepka, Jiřı Šponer, Pavel Banáš
W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model. Journal of chemical theory and computation 17 (6) (2021)
Klaudia Mráziková, Vojtěch Mlýnský, Petra Kührová, Pavlína Pokorná, Holger Kruse, Miroslav Krepl, Michal Otyepka, Pavel Banáš, Jiřı Šponer
UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations. Journal of chemical theory and computation 16 (12) (2020)
Viviana Mollica Nardo, Giuseppe Cassone, Rosina Celeste Ponterio, Franz Saija, Jiřı Šponer, Matteo Tommasini, Sebastiano Trusso
Electric-Field-Induced Effects on the Dipole Moment and Vibrational Modes of the Centrosymmetric Indigo Molecule. The journal of physical chemistry. A 124 (51) (2020)
Donatella Chillè, Giuseppe Cassone, Fausta Giacobello, Ottavia Giuffrè, Viviana Mollica Nardo, Rosina Celeste Ponterio, Franz Saija, Jiřı Šponer, Sebastiano Trusso, Claudia Foti
Removal of As(III) from Biological Fluids: Mono- versus Dithiolic Ligands. Chemical research in toxicology 33 (4) (2020)
Barira Islam, Petr Stadlbauer, Michaela Vorlíčková, Jean-Louis Mergny, Michal Otyepka, Jiřı Šponer
Stability of Two-Quartet G-Quadruplexes and Their Dimers in Atomistic Simulations. Journal of chemical theory and computation 16 (6) (2020)
Vojtěch Mlýnský, Petra Kührová, Tomáš Kühr, Michal Otyepka, Giovanni Bussi, Pavel Banáš, Jiřı Šponer
Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides. Journal of chemical theory and computation 16 (6) (2020)
Petra Vojáčková, Lucyna Michalska, Marek Nečas, Dimitri Shcherbakov, Erik C Böttger, Jiřı Šponer, Judit E Šponer, Jakub Švenda
Stereocontrolled Synthesis of (-)-Bactobolin A. Journal of the American Chemical Society 142 (16) (2020)
Hana Dohnalová, Tomáš Dršata, Jiřı Šponer, Martin Zacharias, Jan Lipfert, Filip Lankaš
Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation. Journal of chemical theory and computation 16 (4) (2020)
Holger Kruse, Klaudia Mrazikova, Luigi D'Ascenzo, Jiřı Šponer, Pascal Auffinger
Short but Weak: The Z-DNA Lone-Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii. Angewandte Chemie (International ed. in English) 59 (38) (2020)
Giuseppe Cassone, Donatella Chillè, Viviana Mollica Nardo, Ottavia Giuffrè, Rosina Celeste Ponterio, Jiřı Šponer, Sebastiano Trusso, Franz Saija, Claudia Foti
Arsenic-nucleotides interactions: an experimental and computational investigation. Dalton transactions (Cambridge, England : 2003) 49 (19) (2020)
Pavlína Pokorná, Miroslav Krepl, Eva Bártová, Jiřı Šponer
Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network. Journal of chemical theory and computation 15 (10) (2019)
Holger Kruse, Jiřı Šponer, Pascal Auffinger
Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis". Journal of chemical information and modeling 59 (9) (2019)
Petra Kührová, Vojtěch Mlýnský, Marie Zgarbová, Miroslav Krepl, Giovanni Bussi, Robert B Best, Michal Otyepka, Jiřı Šponer, Pavel Banáš
Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions". Journal of chemical theory and computation 16 (1) (2019)
Karolina Maria Górecka, Miroslav Krepl, Aleksandra Szlachcic, Jarosław T Poznański, Jiřı Šponer, Marcin Nowotny
RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution. Nature communications 10 (1) (2019)
Andrea Cesari, Sandro Bottaro, Kresten Lindorff-Larsen, Pavel Banáš, Jiřı Šponer, Giovanni Bussi
Fitting Corrections to an RNA Force Field Using Experimental Data. Journal of chemical theory and computation 15 (6) (2019)
Giuseppe Cassone, Donatella Chillè, Fausta Giacobello, Ottavia Giuffrè, Viviana Mollica Nardo, Rosina Celeste Ponterio, Franz Saija, Jiřı Šponer, Sebastiano Trusso, Claudia Foti
Interaction between As(III) and Simple Thioacids in Water: An Experimental and ab Initio Molecular Dynamics Investigation. The journal of physical chemistry. B 123 (28) (2019)
Krishna C Suddala, Ian R Price, Shiba S Dandpat, Michal Janeček, Petra Kührová, Jiřı Šponer, Pavel Banáš, Ailong Ke, Nils G Walter
Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch. Nature communications 10 (1) (2019)
Holger Kruse, Jiřı Šponer
Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking. The journal of physical chemistry. A 123 (42) (2019)
Petra Kührová, Vojtěch Mlýnský, Marie Zgarbová, Miroslav Krepl, Giovanni Bussi, Robert B Best, Michal Otyepka, Jiřı Šponer, Pavel Banáš
Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. Journal of chemical theory and computation 15 (5) (2019)
Jiřı Šponer, Giovanni Bussi, Miroslav Krepl, Pavel Banáš, Sandro Bottaro, Richard A Cunha, Alejandro Gil-Ley, Giovanni Pinamonti, Simón Poblete, Petr Jurečka, Nils G Walter, Michal Otyepka
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chemical reviews 118 (8) (2018)
Holger Kruse, Pavel Banáš, Jiřı Šponer
Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects. Journal of chemical theory and computation 15 (1) (2018)
Rafał Szabla, Holger Kruse, Petr Stadlbauer, Jiřı Šponer, Andrzej L Sobolewski
Sequential electron transfer governs the UV-induced self-repair of DNA photolesions. Chemical science 9 (12) (2018)
Marek Havrila, Petr Stadlbauer, Barira Islam, Michal Otyepka, Jiřı Šponer
Correction to "Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes". Journal of chemical theory and computation 14 (3) (2018)
Pavlína Pokorná, Holger Kruse, Miroslav Krepl, Jiřı Šponer
QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods. Journal of chemical theory and computation 14 (10) (2018)
Barira Islam, Petr Stadlbauer, Miroslav Krepl, Marek Havrila, Shozeb M Haider, Jiřı Šponer
Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations. Journal of chemical theory and computation 14 (10) (2018)
Anna Bochicchio, Miroslav Krepl, Fan Yang, Gabriele Varani, Jiřı Šponer, 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 computational biology 14 (12) (2018)
Sandro Bottaro, Pavel Banáš, Jiřı Šponer, Giovanni Bussi
Correction to "Free Energy Landscape of GAGA and UUCG RNA Tetraloops". The journal of physical chemistry letters 9 (7) (2018)
Raffaele Saladino, Judit E Sponer, Jiřı Šponer, Ernesto Di Mauro
Rewarming the Primordial Soup: Revisitations and Rediscoveries in Prebiotic Chemistry. Chembiochem : a European journal of chemical biology 19 (1) (2017)
Marie Zgarbová, Petr Jurečka, Jiřı Šponer, Michal Otyepka
A- to B-DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker. Journal of chemical theory and computation 14 (1) (2017)