Výpis publikací

ZHANG, Zhengyue, Jiří ŠPONER, Giovanni BUSSI, Vojtěch MLÝNSKÝ, Petr ŠULC, Chad R. SIMMONS, Nicholas STEPHANOPOULOS a Miroslav KREPL. Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of Chemical Information and Modeling. 1549-960X: American Chemical Society, 2023, roč. 63, č. 9, s. 2794-2809. ISSN 1549-9596. Dostupné z: https://dx.doi.org/10.1021/acs.jcim.3c00358.

VÖGELE, Jennifer, Elke DUCHARDT-FERNER, Holger KRUSE, Zhengyue ZHANG, Jiří ŠPONER, Miroslav KREPL a Jens WÖHNERT. Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA. RNA. Cold Spring Harbor Laboratory Press, 2023, roč. 29, č. 6, s. 790-807. ISSN 1355-8382. Dostupné z: https://dx.doi.org/10.1261/rna.079506.122.

POKORNÁ, Pavlína, Miroslav KREPL, Sébastien CAMPAGNE a Jiří ŠPONER. Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations. Journal of Physical Chemistry B. American Chemical Society, 2022, roč. 126, č. 45, s. 9207-9221. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.2c06168.

MRÁZIKOVÁ, Klaudia, Pascal AUFFINGER, Jiří ŠPONER a Holger KRUSE. Lone-pair...π Contacts in Nucleic Acids: Revision of Lennard-Jones Parameters Needed. In Virtual Winter School on Computational Chemistry. 2022.

JANICKI, Mikolaj J., Rafal Kazimierz SZABLA, Jiří ŠPONER a Robert W. GORA. Photoinduced water-chromophore electron transfer causes formation of guanosine photodamage. Physical Chemistry Chemical Physics. Royal Society of Chemistry, 2022, roč. 24, č. 14, s. 8217-8224. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/d2cp00801g.

MRÁZIKOVÁ, Klaudia, Pascal AUFFINGER, Holger KRUSE, Vojtěch MLÝNSKÝ a Jiří ŠPONER. Quantum chemistry reveals AMBER force field shortcomings for anion…π contacts in nucleic acids. In 2nd International Conference on Noncovalent Interactions. 2022.

MRÁZIKOVÁ, Klaudia, Pascal AUFFINGER, Holger KRUSE, Vojtěch MLÝNSKÝ a Jiří ŠPONER. Quantum chemistry reveals AMBER force field shortcomings for anion…π contacts in nucleic acids. In WATOC 2020: 12th Triennial Congress of the World Association of Theoretical and Computational Chemists. 2022.

KREPL, Miroslav, Pavlína POKORNÁ, Vojtěch MLÝNSKÝ, Petr STADLBAUER a Jiří ŠPONER. Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field. Nucleic Acids Research. Oxford University Press, 2022, roč. 50, č. 21, s. 12480-12496. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkac1106.

LENARČIČ ŽIVKOVIĆ, Martina, Martin GAJARSKÝ, Kateřina BEKOVÁ, P. STADLBAUER, Lukáš VICHEREK, M. PETROVA, Radovan FIALA, I. ROSENBERG, Jiří ŠPONER, J. PLAVEC a Lukáš TRANTÍREK. Insight into formation propensity of pseudocircular DNA G-hairpins. Nucleic acids research. Oxford: Oxford University Press, 2021, roč. 49, č. 4, s. 2317-2332. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkab029.

ŠPONEROVÁ, Judit, Jiří ŠPONER, Jakub VÝRAVSKÝ, Ondrej ŠEDO, Zbyněk ZDRÁHAL, Giovanna COSTANZO, Ernesto DI MAURO, Sreekar WUNNAVA, Dieter BRAUN, Roman MATYÁŠEK a Aleš KOVAŘÍK. Nonenzymatic, Template-Free Polymerization of 3',5' Cyclic Guanosine Monophosphate on Mineral Surfaces. ChemSystemsChem. Wiley, 2021, roč. 3, č. 6, s. "e2100017", 8 s. ISSN 2570-4206. Dostupné z: https://dx.doi.org/10.1002/syst.202100017.

ZHANG, Zhengyue, J. VOGELE, Klaudia MRÁZIKOVÁ, H. KRUSE, X.H. CANG, J. WOHNERT, M. KREPL a Jiří ŠPONER. Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments. Journal of Physical Chemistry B. Washington, D.C.: American Chemical Society, 2021, roč. 125, č. 3, s. 825-840. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.0c10192.

ŠPONEROVÁ, Judit, Jiří ŠPONER, Aleš KOVAŘÍK, Ondrej ŠEDO, Zbyněk ZDRÁHAL, Giovanna COSTANZO a Ernesto DI MAURO. Questions and Answers Related to the Prebiotic Production of Oligonucleotide Sequences from 3′,5′ Cyclic Nucleotide Precursors. Life. 2021, roč. 11, č. 8, s. "800", 13 s. ISSN 2075-1729. Dostupné z: https://dx.doi.org/10.3390/life11080800.

POKORNÁ, Pavlína, Miroslav KREPL a Jiří ŠPONER. Residues flanking the ARK^me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations. Biochimica et Biophysica Acta - General Subjects. Amsterdam: Elsevier B.V., 2021, roč. 1865, č. 1, s. 1-12. ISSN 0304-4165. Dostupné z: https://dx.doi.org/10.1016/j.bbagen.2020.129771.

MRÁZIKOVÁ, Klaudia, Pascal AUFFINGER, Jiří ŠPONER, Vojtěch MLÝNSKÝ a Holger KRUSE. Revealing Short-Range Imbalances in AMBER Force Field for Lone-pair…π Contacts. In RNA 2021. 2021.

ŠKOLÁKOVÁ, Petra, Zahra BADRI, Silvie TRANTÍRKOVÁ, Jan RYNEŠ, Jiří ŠPONER, Miloslava FOJTOVÁ, Jiří FAJKUS, Radek MAREK, Michaela VORLÍČKOVÁ, Jean-Louis MERGNY a Lukáš TRANTÍREK. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. BBA - General Subjects. Elsevier B.V., 2020, roč. 1864, č. 9, s. 129651-129659. ISSN 0304-4165. Dostupné z: https://dx.doi.org/10.1016/j.bbagen.2020.129651.

KRUSE, Holger, Klaudia MRÁZIKOVÁ, Luigi D'ASCENZO, Jiří ŠPONER a Pascal AUFFINGER. Short but Weak: The Z-DNA lone-pair...Pi Conundrum Challenges Standard Carbon Van der Waals Radii. Angewandte Chemie International Edition. Weinheim: Wiley-VCH Verlag, 2020, roč. 59, č. 38, s. 16553-16560. ISSN 1433-7851. Dostupné z: https://dx.doi.org/10.1002/anie.202004201.

VOJÁČKOVÁ, Petra, Lucyna MICHALSKA, Marek NEČAS, Dimitri SHCHERBAKOV, Erik C. BÖTTGER, Jiří ŠPONER, Judit E. ŠPONER a Jakub ŠVENDA. Stereocontrolled Synthesis of (-)-Bactobolin A. Journal of the American Chemical Society. Washington: American Chemical Society, 2020, roč. 142, č. 16, s. 7306-7311. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/jacs.0c01554.

POKORNÁ, Pavlína, Jiří ŠPONER, Miroslav KREPL a Eva BÁRTOVÁ. Atomic Details on Protein-Protein Recognition - Role of Side Chain Dynamics in Binding Between HP1 and H3 Proteins. In PhD Joint Retreat. 2019. ISBN 978-80-210-9301-0.

LEGARTOVÁ, Sofia, Gabriela LOCHMANOVÁ, Zbyněk ZDRÁHAL, Stanislav KOZUBEK, Jiří ŠPONER, Miroslav KREPL, Pavlína POKORNÁ a Eva BÁRTOVÁ. DNA Damage Changes Distribution Pattern and Levels of HP1 Protein Isoforms in the Nucleolus and Increases Phosphorylation of HP1 beta-Ser88. CELLS. 2019, roč. 8, č. 9, s. "1097", 22 s. ISSN 2073-4409. Dostupné z: https://dx.doi.org/10.3390/cells8091097.

MRÁZIKOVÁ, Klaudia, Holger KRUSE, Jiří ŠPONER a Pascal AUFFINGER. Lone pair-π and anion-π interactions as stabilization factors of RNA tetraloops. In PhD Joint Retreat. 2019. ISBN 978-80-210-9301-0.

MRÁZIKOVÁ, Klaudia, Holger KRUSE, Jiří ŠPONER a Pascal AUFFINGER. Lone pair-π and anion-π interactions as stabilization factors of RNA tetraloops. In XIXth Interdisciplinary Meeting of Young Life Scientists. 2019. ISSN 2336-7210.

STADLBAUER, P., P. KUHROVA, Lukáš VICHEREK, P. BANAS, M. OTYEPKA, Lukáš TRANTÍREK a Jiří ŠPONER. Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. Nucleic acids research. Oxford: Oxford University Press, 2019, roč. 47, č. 14, s. 7276-7293. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkz610.

FERUS, M., F. PIETRUCCI, A.M. SAITTA, O. IVANEK, A. KNIZEK, P. KUBELIK, M. KRUS, L. JUHA, R. DUDZAK, J. DOSTAL, A. PASTOREK, L. PETERA, J. HRNCIROVA, H. SAEIDFIROZEH, V. SHESTIVSKA, Jiří ŠPONER, J.E. SPONER, P. RIMMER, S. CIVIS a G. CASSONE. Prebiotic synthesis initiated in formaldehyde by laser plasma simulating high-velocity impacts. ASTRONOMY & ASTROPHYSICS. LES ULIS CEDEX A: EDP SCIENCES S A, 2019, roč. 626, JUN, s. 1-21. ISSN 1432-0746. Dostupné z: https://dx.doi.org/10.1051/0004-6361/201935435.

POKORNÁ, Pavlína, Miroslav KREPL, Jiří ŠPONER, Klaudia MRÁZIKOVÁ, Vojech MLYNSKY a Holger KRUSE. QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods. In RNA 2019. 2019.

KRUSE, H. a Jiří ŠPONER. Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking. Journal of Physical Chemistry A. WASHINGTON: AMER CHEMICAL SOC, 2019, roč. 123, č. 42, s. 9209-9222. ISSN 1089-5639. Dostupné z: https://dx.doi.org/10.1021/acs.jpca.9b05940.

POKORNÁ, Pavlína, Miroslav KREPL, E. BARTOVA a Jiří ŠPONER. Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1 gamma(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2019, roč. 15, č. 10, s. 5659-5673. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.9b00434.

POKORNÁ, Pavlína, Holger KRUSE, Miroslav KREPL a Jiří 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. Washington DC: American Chemical Society, 2018, roč. 14, č. 10, s. 5419-5433. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.8b00670.

XU, Jianfeng, Maria TSANAKOPOULOU, Christopher J. MAGNANI, Rafal SZABLA, Judit ŠPONEROVÁ, Jiří ŠPONER, Robert W. GORA a John D. SUTHERLAND. A prebiotically plausible synthesis of pyrimidine beta-ribonucleosides and their phosphate derivatives involving photoanomerization. Nature chemistry. London: Nature Publishing Group, 2017, roč. 9, č. 4, s. 303-309. ISSN 1755-4330. Dostupné z: https://dx.doi.org/10.1038/NCHEM.2664.

DIARRA DIT KONTÉ, Nana, Miroslav KREPL, Fred DAMBERGER, N RIPPIN, O DUSS, Jiří ŠPONER a Allain FRÉDÉRIC. Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination. NATURE COMMUNICATIONS. Nature Publishing Group, 2017, roč. 8, s. e654. ISSN 2041-1723. Dostupné z: https://dx.doi.org/10.1038/s41467-017-00631-3.

FIGIEL, M, Miroslav KREPL, J POZNANSKI, A GOTAB, Jiří ŠPONER a Marcin NOWOTNY. Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase. Nucleic Acids Research. Oxford: Oxford University Press, 2017, roč. 45, č. 6, s. 3341-3352. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkx004.

HAVRILA, Marek, P. STADLBAUER, B. ISLAM, M. OTYEPKA a Jiří ŠPONER. Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2017, roč. 13, č. 8, s. 3911-3926. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.7b00267.

ISLAM, Barira, Petr STADLBAUER, Alejandro GIL-LEY, Guillermo PEREZ-HERNANDEZ, Shozeb HAIDER, Stephen NEIDLE, Giovanni BUSSI, Pavel BANAS, Michal OTYEPKA a Jiří ŠPONER. Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2017. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.7b00226.

ŠPONER, Jiří, Giovanni BUSSI, Petr STADLBAUER, Petra KUHROVA, Pavel BANÁŠ, Barira ISLAM, Shozeb HAIDER, Stephen NEIDLE a Michal OTYEPKA. Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochimica et Biophysica Acta (BBA) - General Subjects. 2017, roč. 1861, č. 5, s. 1246–1263. ISSN 0006-3002. Dostupné z: https://dx.doi.org/10.1016/j.bbagen.2016.12.008.

ŠPONER, Jiří, Miroslav KREPL, Pavel BANÁŠ, P KUHROVA, Marie ZGARBOVÁ, Petr JUREČKA, Marek HAVRILA a Michal OTYEPKA. How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes? Wiley Interdisciplinary Reviews: RNA. Hoboken, USA: WILEY-BLACKWELL, 2017, roč. 8, č. 3, 17 s. ISSN 1757-7004. Dostupné z: https://dx.doi.org/10.1002/wrna.1405.

GRESH, Nohad, Sehr NASEEM-KHAN, Louis LAGARDERE, Jean-Philip PIQUEMAL, Judit ŠPONEROVÁ a Jiří ŠPONER. Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li+, Na+, K+, and Rb+ Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2017, roč. 121, č. 16, s. 3997-4014. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.7b01836.

POKORNÁ, Pavlína, Miroslav KREPL, Holger KRUSE a Jiří ŠPONER. MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, L-Histidine Ligand, and Mg2+. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2017, roč. 13, č. 11, s. 5658-5670. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.7b00598.

DRSATA, Tomas, Kamila RÉBLOVÁ, Ivana BESSEOVA, Jiří ŠPONER a Filip LANKAS. rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2017, roč. 13, č. 7, s. 3359-3371. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.7b00061.

NOUREINI, Sakineh Kazemi, Hosein ESMAEILI, Farzane ABACHI, Soraia KHIALI, Barira ISLAM, Martyna KUTA, Ali A. SABOURY, Marcin HOFFILLANN, Jiří ŠPONER, Gary PARKINSON a Shozeb HAIDER. Selectivity of major isoquinoline alkaloids from Chelidonium majus towards telomeric G-quadruplex: A study using a transition-FRET (t-FRET) assay. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS. AMSTERDAM: ELSEVIER SCIENCE BV, 2017, roč. 1861, č. 8, s. 2020-2030. ISSN 0304-4165. Dostupné z: https://dx.doi.org/10.1016/j.bbagen.2017.05.002.

KREPL, Miroslav, Markus BLATTER, Antoine CLERY, Fred F DAMBERGER, Frederic H T ALLAIN a Jiří ŠPONER. Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition. Nucleic acids research. Oxford University Press, 2017. ISSN 1362-4962. Dostupné z: https://dx.doi.org/10.1093/nar/gkx418.

GAJARSKÝ, Martin, Martina Lenarcic ZIVKOVIC, Petr STADLBAUER, Bruno PAGANO, Radovan FIALA, Jussara AMATO, L´ubomir TOMASKA, Jiří ŠPONER, Janez PLAVEC a Lukáš TRANTÍREK. Structure of a Stable G-Hairpin. Journal of the American Chemical Society. WASHINGTON: American Chemical Society, 2017, roč. 139, č. 10, s. 3591-3594. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/jacs.6b10786.

KREPL, Miroslav, Antoine CLERY, Markus BLATTER, Frederic ALLAIN a Jiří ŠPONER. Study of Fox-1 and SRSF1 RRMs - the molecular recognition and hydration. In 22nd Annual Meeting of the RNA Society. 2017.

GALINDO-MURILLO, Rodrigo, James C. ROBERTSON, Marie ZGARBOVÁ, Jiří ŠPONER, Michal OTYEPKA, Petr JUREČKA a Thomas E. CHEATHAM. Assessing the Current State of Amber Force Field Modifications for DNA. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2016, roč. 12, č. 8, s. 4114-4127. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.6b00186.

ISLAM, Barira, Petr STADLBAUER, Stephen NEIDLE, Shozeb HAIDER a Jiří ŠPONER. Can We Execute Reliable MM-PBSA Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds? Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2016, roč. 120, č. 11, s. 2899-2912. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.6b01059.

STADLBAUER, Petr, L MAZZANTI, T CRAGNOLINI, DJ WALES, P DERREUMAUX, S PASQUALI a Jiří ŠPONER. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2016, roč. 12, č. 12, s. 6077-6097. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.6b00667.

SZABLA, Rafal, Marek HAVRILA, Holger KRUSE a Jiří ŠPONER. Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2016, roč. 120, č. 41, s. 10635-10648. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.6b07551.

ZHANG, Xiaojun, Cui-Xia XU, Rosa DI FELICE, Jiří ŠPONER, Barira ISLAM, Petr STADLBAUER, Yuan DING, Lingling MAO, Zong-Wan MAO a Peter Z. QIN. Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label. Biochemistry. WASHINGTON: AMER CHEMICAL SOC, 2016, roč. 55, č. 2, s. 360-372. ISSN 0006-2960. Dostupné z: https://dx.doi.org/10.1021/acs.biochem.5b01189.

GKIONIS, Konstantinos, Holger KRUSE a Jiří ŠPONER. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2016, roč. 12, č. 4, s. 2000-2016. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.5b01025.

ŠPONEROVÁ, Judit, Jiří ŠPONER, Olga NOVÁKOVÁ, Viktor BRABEC, Ondrej ŠEDO, Zbyněk ZDRÁHAL, Giovanna COSTANZO, Samanta PINO, Raffaele SALADINO a Ernesto DI MAURO. Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario. Chemistry - A European Journal. WEINHEIM: Wiley, 2016, roč. 22, č. 11, s. 3572-3586. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201503906.

ŠPONEROVÁ, Judit, Jiří ŠPONER a Ernesto DI MAURO. Four Ways to Oligonucleotides Without Phosphoimidazolides. Journal of molecular evolution. New York: Springer, 2016, roč. 82, č. 1, s. 5-10. ISSN 0022-2844. Dostupné z: https://dx.doi.org/10.1007/s00239-015-9709-5.

REBIČ, Matúš, Aatto LAAKSONEN, Jiří ŠPONER, Jozef ULIČNÝ a Francesca MOCCI. Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2016, roč. 120, č. 30, s. 7380-7391. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.6b06485.

COSTANZO, Giovanna, Samanta PINO, Anna Maria TIMPERIO, Judit ŠPONEROVÁ, Jiří ŠPONER, Olga NOVAKOVA, Ondrej ŠEDO, Zbyněk ZDRÁHAL a Ernesto DI MAURO. Non-Enzymatic Oligomerization of 3 ', 5 ' Cyclic AMP. Plos one. San Francisco: Public Library of Science, 2016, roč. 11, č. 11, s. nestránkováno, 14 s. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0165723.

DRŠATA, Tomáš, Marie ZGARBOVÁ, Petr JUREČKA, Jiří ŠPONER a Filip LANKAŠ. On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA. Biophysical Journal. Cambridge: Cell Press, 2016, roč. 110, č. 4, s. 874-876. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2015.12.039.

SZABLA, Rafal, Robert W. GORA, Mikolaj JANICKI a Jiří ŠPONER. Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires. FARADAY DISCUSSIONS. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2016, roč. 195, č. 2016, s. 237-251. ISSN 1359-6640. Dostupné z: https://dx.doi.org/10.1039/c6fd00131a.

ŠPONEROVÁ, Judit, Rafal Kazimierz SZABLA, Robert W. GORA, A. Marco SAITTA, Fabio PIETRUCCI, Franz SAIJA, Ernesto DI MAURO, Raffaele SALADINO, Martin FERUS, Svatopluk CIVIŠ a Jiří ŠPONER. Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments. Physical Chemistry Chemical Physics. Cambridge: Royal Society of Chemistry, 2016, roč. 18, č. 30, s. 20047-20066. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c6cp00670a.

KREPL, Miroslav, Antoine CLERY, Markus BLATTER, Frederic H. T. ALLAIN a Jiří ŠPONER. Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs. Nucleic Acids Research. Oxford: Oxford University Press, 2016, roč. 44, č. 13, s. 6452-6470. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkw438.

CIVIŠ, Svatopluk, Rafal Kazimierz SZABLA, Bartłomiej M. SZYJA, Daniel SMYKOWSKI, Ondřej IVANEK, Antonín KNÍŽEK, Petr KUBELÍK, Jiří ŠPONER, Martin FERUS a Judit ŠPONEROVÁ. TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth. Scientific Reports. LONDON: NATURE PUBLISHING GROUP, 2016, roč. 6, March, s. nestránkováno, 7 s. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/srep23199.

SZABLA, Rafal Kazimierz, Robert W. GORA a Jiří ŠPONER. Ultrafast excited-state dynamics of isocytosine. Physical Chemistry Chemical Physics. Cambridge: Royal Society of Chemistry, 2016, roč. 18, č. 30, s. 20208-20218. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c6cp01391k.

OHNMACHT, Stephan A., Chiara MARCHETTI, Mekala GUNARATNAM, Rachael J. BESSER, Shozeb M. HAIDER, Gloria DI VITA, Helen L. LOWE, Maria MELLINAS-GOMEZ, Seckou DIOCOU, Mathew ROBSON, Jiří ŠPONER, Barira ISLAM, R. Barbara PEDLEY, John A. HARTLEY a Stephen NEIDLE. A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer. Scientific Reports. London: Nature Publishing Group, 2015, roč. 5, june, s. "nestránkováno", 11 s. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/srep11385.

KREPL, Miroslav, Marek HAVRILA, Petr STADLBAUER, Pavel BANÁŠ, Michal OTYEPKA, Josef PASULKA, Richard ŠTEFL a Jiří ŠPONER. Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 11, č. 3, s. 1220-1243. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct5008108.

PANECKA, Joanna, Jiří ŠPONER a Joanna TRYLSKA. Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site. Biochimie. Paris: Elsevier France- editions Scientifiques Medicales Elsevier, 2015, roč. 112, May, s. 96-110. ISSN 0300-9084. Dostupné z: https://dx.doi.org/10.1016/j.biochi.2015.02.021.

SZABLA, Rafal Kazimierz, Jiří ŠPONER a Robert W. GORA. Electron-Driven Proton Transfer Along H2O Wires Enables Photorelaxation of pi sigma* States in Chromophore-Water Clusters. Journal of Physical Chemistry Letters. Washington: American Chemical Society, 2015, roč. 6, č. 8, s. 1467-1471. ISSN 1948-7185. Dostupné z: https://dx.doi.org/10.1021/acs.jpclett.5b00261.

SZABLA, Rafal Kazimierz, Jesus CAMPOS, Judit ŠPONEROVÁ, Jiří ŠPONER, Robert W. GORA a John D. SUTHERLAND. Excited-state hydrogen atom abstraction initiates the photochemistry of beta-2 '-deoxycytidine. CHEMICAL SCIENCE. Cambridge: ROYAL SOC CHEMISTRY, 2015, roč. 6, č. 3, s. 2035-2043. ISSN 2041-6520. Dostupné z: https://dx.doi.org/10.1039/c4sc03761h.

ISLAM, Barira, Petr STADLBAUER, Miroslav KREPL, Jaroslav KOČA, Stephen NEIDLE, Shozeb HAIDER a Jiří ŠPONER. Extended molecular dynamics of a c-kit promoter quadruplex. Nucleic Acids Research. Oxford: Oxford University Press, 2015, roč. 43, č. 18, s. 8673-8693. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkv785.

STADLBAUER, Petr, Petra KUHROVÁ, Pavel BANÁŠ, Jaroslav KOČA, Giovanni BUSSI, Lukáš TRANTÍREK, Michal OTYEPKA a Jiří ŠPONER. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic Acids Research. Oxford: Oxford University Press, 2015, roč. 43, č. 20, s. 9626-9644. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkv994.

FERUS, Martin, David NESVORNÝ, Jiří ŠPONER, Petr KUBELÍK, Regina MICHALČÍKOVÁ, Violetta SHESTIVSKÁ, Judit ŠPONEROVÁ a Svatopluk CIVIŠ. High-energy chemistry of formamide: A unified mechanism of nucleobase formation. Proceedings of the National Academy of Sciences of the United States of America. Washington D.C.: NATL ACAD SCIENCES, 2015, roč. 112, č. 3, s. 657-662. ISSN 0027-8424. Dostupné z: https://dx.doi.org/10.1073/pnas.1412072111.

DUBECKÝ, Matúš, Nils G. WALTER, Jiří ŠPONER, Michal OTYEPKA a Pavel BANÁŠ. Chemical Feasibility of the General Acid/Base Mechanism of glmS Ribozyme Self-Cleavage. Biopolymers. Hoboken: WILEY-BLACKWELL, 2015, roč. 103, č. 10, s. 550-562. ISSN 0006-3525. Dostupné z: https://dx.doi.org/10.1002/bip.22657.

ISLAM, Barira, Petr STADLBAUER, Shozeb HAIDER a Jiří ŠPONER. Insights from 10 μs-scale molecular dynamics simulations of human telomeric quadruplexes. In 5th International Meeting on Quadruplex Nucleic Acids: G4thering in Bordeaux. 2015.

HALDAR, Susanta, Petra KUHROVÁ, Pavel BANÁŠ, Vojtěch SPIWOK, Jiří ŠPONER, Pavel HOBZA a Michal OTYEPKA. Insights into Stability and Folding of GNRA and UNCG Tetra loops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 11, č. 8, s. 3866-3877. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.5b00010.

STADLBAUER, Petr a Jiří ŠPONER. Intermediates in Folding of Human Telomeric Quadruplexes Studied by Molecular Dynamics Simulations. In 5th International Meeting on Quadruplex Nucleic Acids: G4thering in Bordeaux. 2015.

HAVRILA, Marek, Marie ZGARBOVÁ, Petr JUREČKA, Pavel BANÁŠ, Miroslav KREPL, Michal OTYEPKA a Jiří ŠPONER. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 119, č. 49, s. 15176-15190. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.5b08876.

ESTARELLAS MARTIN, Carolina, Michal OTYEPKA, Jaroslav KOČA, Pavel BANÁŠ, Miroslav KREPL a Jiří ŠPONER. Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS. AMSTERDAM: ELSEVIER SCIENCE BV, 2015, roč. 1850, č. 5, s. 1072-1090. ISSN 0304-4165. Dostupné z: https://dx.doi.org/10.1016/j.bbagen.2014.10.021.

KRUSE, Holger, Arnošt MLÁDEK, Konstantinos GKIONIS, Andreas HANSEN, Sstefan GRIMME a Jiří ŠPONER. Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2015, roč. 11, č. 10, s. 4972-4991. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.5b00515.

FERUS, Martin, Antonín KNÍŽEK, Jiří ŠPONER, Judit ŠPONEROVÁ a Svatopluk CIVIŠ. RADIKÁLOVÁ SYNTÉZA NUKLEOVÝCH BÁZÍ Z FORMAMIDU V IMPAKTNÍM PLAZMATU. CHEMICKÉ LISTY. Praha: Česká společnost chemická, 2015, roč. 109, č. 6, s. 406-414. ISSN 0009-2770.

MLÝNSKÝ, Vojtěch, Petra KÜHROVÁ, Marie ZGARBOVÁ, Petr JUREČKA, Nils G. WALTER, Michal OTYEPKA, Jiří ŠPONER a Pavel BANÁŠ. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations. Journal of Physical Chemistry B. Washington D.C.: AMER CHEMICAL SOC, 2015, roč. 119, č. 11, s. 4220-4229. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp512069n.

ZGARBOVÁ, M., Jiří ŠPONER, Michal OTYEPKA, T.E. CHEATHAM, R. GALINDO-MURILLO a P. JUREČKA. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2015, roč. 11, č. 12, s. 5723-5736. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.5b00716.

GRESH, Nohad, Judit ŠPONEROVÁ, Mike DEVEREUX, Konstantinos GKIONIS, Benoit COURCY DE, Jean-Philip PIQUEMAL a Jiří ŠPONER. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 119, č. 30, s. 9477-9495. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.5b01695.

STADLBAUER, Petr, Jiří ŠPONER, Giovanna COSTANZO, Ernesto DI MAURO, Samanta PINO a Judit ŠPONEROVÁ. Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides. Chemistry - A European Journal. WEINHEIM: WILEY-VCH, 2015, roč. 21, č. 9, s. 3596-3604. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201406140.

MLÝNSKÝ, Vojtěch, Nils G. WALTER, Jiří ŠPONER, Michal OTYEPKA a Pavel BANÁŠ. The role of an active site Mg2+ in HDV ribozyme self-cleavage: Insights from QM/MM calculations. Physical Chemistry Chemical Physics. Cambridge: Royal Society of Chemistry, 2015, roč. 17, č. 1, s. 670-679. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c4cp03857f.

KRUSE, Holger a Jiří ŠPONER. Towards biochemically relevant QM computations on nucleic acids: controlled electronic structure geometry optimization of nucleic acid structural motifs using penalty restraint functions. Physical Chemistry Chemical Physics. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2015, roč. 17, č. 2, s. 1399-1410. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c4cp04680c.

ŠPONEROVÁ, Judit, Jiří ŠPONER, Alessandra GIORGI, Ernesto DI MAURO, Samanta PINO a Giovanna COSTANZO. Untemplated Nonenzymatic Polymerization of 3 ',5 ' cGMP: A Plausible Route to 3 ',5 '-Linked Oligonucleotides in Primordia. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 119, č. 7, s. 2979-2989. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.5b00601.

SRIPATHI, Kamali N., Pavel BANÁŠ, Kamila RÉBLOVÁ, Jiří ŠPONER, Michal OTYEPKA a Nils G. WALTER. Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics. Physical Chemistry Chemical Physics. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2015, roč. 17, č. 8, s. 5887-5900. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c4cp05083e.

KUEHROVA, Petra, Michal OTYEPKA, Jiří ŠPONER a Pavel BANÁŠ. Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2014, roč. 10, č. 1, s. 401-411. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct400663s.

ZGARBOVÁ, Marie, Michal OTYEPKA, Jiří ŠPONER, Filip LANKAŠ a Petr JUREČKA. Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA. Journal of Chemical Theory and Computation. Washington: American Chemical Society, 2014, roč. 10, č. 8, s. 3177-3189. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct500120v.

MLÝNSKÝ, Vojtěch, Pavel BANÁŠ, Jiří ŠPONER, Marc W. VAN DER KAMP, Adrian J. MULHOLLAND a Michal OTYEPKA. Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2014, roč. 10, č. 4, s. 1608-1622. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct401015e.

SRIPATHI, Kamali N., Wendy W. TAY, Pavel BANÁŠ, Michal OTYEPKA, Jiří ŠPONER a Nils G. WALTER. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. RNA. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 2014, roč. 20, č. 7, s. 1112-1128. ISSN 1355-8382. Dostupné z: https://dx.doi.org/10.1261/rna.044982.114.

MLÁDEK, Arnošt, Pavel BANÁŠ, Petr JUREČKA, Michal OTYEPKA, Marie ZGARBOVÁ a Jiří ŠPONER. Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2014, roč. 10, č. 1, s. 463-480. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct400837p.

FERUS, Martin, Regina MICHALČÍKOVÁ, Violetta SHESTIVSKÁ, Jiří ŠPONER, Judit ŠPONEROVÁ a Svatopluk CIVIŠ. High-Energy Chemistry of Formamide: A Simpler Way for Nucleobase Formation. Journal of Physical Chemistry A. Washington DC: American Chemical Society, 2014, roč. 118, č. 4, s. 719-736. ISSN 1089-5639. Dostupné z: https://dx.doi.org/10.1021/jp411415p.

GKIONIS, Konstantinos, Holger KRUSE, James PLATTS, Arnošt MLÁDEK, Jaroslav KOČA a Jiří ŠPONER. Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2014, roč. 10, č. 3, s. 1326-1340. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct4009969.

DRŠATA, Tomáš, Marie ZGARBOVÁ, Naděžda ŠPAČKOVÁ, Petr JUREČKA, Jiří ŠPONER a Filip LANKAŠ. Mechanical Model of DNA Allostery. Journal of Physical Chemistry Letters. Washington: American Chemical Society, 2014, roč. 5, č. 21, s. 3831-3835. ISSN 1948-7185. Dostupné z: https://dx.doi.org/10.1021/jz501826q.

DRSATA, Tomáš, Naďa ŠPAČKOVÁ, Petr JUREČKA, Marie ZGARBOVÁ, Jiří ŠPONER a Filip LANKAŠ. Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. Nucleic Acids Research. Oxford: Oxford University Press, 2014, roč. 42, č. 11, s. 7383-7394. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gku338.

ŠPONER, Jiří, Pavel BANÁŠ, Petr JUREČKA, Marie ZGARBOVÁ, Petra KÜHROVÁ, Marek HAVRILA, Miroslav KREPL, Petr STADLBAUER a Michal OTYEPKA. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. The Journal of Physical Chemistry Letters. Washington: American Chemical Society, 2014, roč. 5, č. 10, s. 1771-1782. ISSN 1948-7185. Dostupné z: https://dx.doi.org/10.1021/jz500557y.

SZABLA, Rafal Kazimierz, Robert W. GÓRA, Jiří ŠPONER a Judit ŠPONEROVÁ. Molecular Mechanism of Diaminomaleonitrile to Diaminofumaronitrile Photoisomerization: An Intermediate Step in the Prebiotic Formation of Purine Nucleobases. Chemistry - A European Journal. Weinheim: WILEY- VCH VERLAG GMBH, 2014, roč. 20, č. 9, s. 2515-2521. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201304224.

PASI, Marco, John H. MADDOCKS, David BEVERIDGE, Thomas C. BISHOP, David A. CASE, Thomas CHEATHAM III., Pablo D. DANS, B. JAYARAM, Filip LANKAŠ, Charles LAUGHTON, Jonathan MITCHELL, Roman OSMAN, Modesto OROZCO, Alberto PÉREZ, Daiva PETKEVIČIÜTÉ, Naďa ŠPAČKOVÁ, Jiří ŠPONER, Krystyna ZAKRZEWSKA a Richard LAVERY. muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research. Oxford: Oxford University Press, 2014, roč. 42, č. 19, s. 12272-12283. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gku855.

KRUSE, Holger, Marek HAVRILA a Jiří ŠPONER. QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches. Journal of Chemical Theory and Computation. Washington: American Chemical Society, 2014, roč. 10, č. 6, s. 2615-2629. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct500183w.

PANECKA, Joanna, Marek HAVRILA, Kamila RÉBLOVÁ, Jiří ŠPONER a Joanna TRYLSKA. Role of S-turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A-Site. A Bioinformatics and Molecular Dynamics Simulation Study. Journal of Physical Chemistry B. WASHINGTON: American Chemical Society, 2014, roč. 118, č. 24, s. 6687-6701. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp5030685.

CIVIŠ, Svatopluk, Martin FERUS, Judit ŠPONEROVÁ, Jiří ŠPONER, Ladislav KAVAN a Markéta ZUKALOVÁ. Room temperature spontaneous conversion of OCS to CO2 on the anatase TiO2 surface. Chemical Communications. Cambridge: Royal Society of Chemistry, 2014, roč. 50, č. 57, s. 7712-7715. ISSN 1359-7345. Dostupné z: https://dx.doi.org/10.1039/c4cc01992j.

SZABLA, Rafal Kazimierz, Judit ŠPONEROVÁ, Jiří ŠPONER, Andrzej SOBOLEWSKI a Robert W. GÓRA. Solvent effects on the photochemistry of 4-aminoimidazole-5-carbonitrile, a prebiotically plausible precursor of purines. Physical Chemistry Chemical Physics. Cambridge: Royal Society of Chemistry, 2014, roč. 16, č. 33, s. 17617-17626. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c4cp02074j.

STADLBAUER, Petr, Lukáš TRANTÍREK, Thomas E. CHEATHAM III., Jaroslav KOČA a Jiří ŠPONER. Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations. Biochimie. Paris: ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER, 2014, roč. 105c, October, s. 22-35. ISSN 0300-9084. Dostupné z: https://dx.doi.org/10.1016/j.biochi.2014.07.009.

MLÁDEK, Arnošt, Miroslav KREPL, Daniel SVOZIL, Petr CECH, Michal OTYEPKA, Pavel BANÁŠ, Marie ZGARBOVA, Petr JURECKA a Jiří ŠPONER. Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory. Physical Chemistry Chemical Physics. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2013, roč. 15, č. 19, s. 7295-7310. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c3cp44383c.

KREPL, Miroslav, Kamila RÉBLOVÁ, Jaroslav KOČA a Jiří ŠPONER. Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops. JOURNAL OF PHYSICAL CHEMISTRY B. Washington: American Chemical Society, 2013, roč. 117, č. 18, s. 5540-5555. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp401482m.

KUHROVA, Petra, Pavel BANÁŠ, Robert B BEST, Jiří ŠPONER a Michal OTYEPKA. Computer Folding of RNA Tetraloops? Are We There Yet? Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2013, roč. 9, č. 4, s. 2115-2125. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct301086z.

ISLAM, Barira, Miriam SGOBBA, Charlie LAUGHTON, Modesto OROZCO, Jiří ŠPONER, Stephen NEIDLE a Shozeb HAIDER. Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. Nucleic Acids Research. Oxford, UK: Oxford Press, 2013, roč. 41, č. 4, s. 2723-2735. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gks1331.

KREPL, Miroslav, Michal OTYEPKA, Pavel BANÁŠ a Jiří ŠPONER. Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study. JOURNAL OF PHYSICAL CHEMISTRY B. Washington: American Chemical Society, 2013, roč. 117, č. 6, s. 1872-1879. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp311180u.

ŠPONER, Jiří, Judit ŠPONEROVÁ, Arnošt MLÁDEK, Pavel BANÁŠ, Petr JURECKA a Michal OTYEPKA. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods. SAN DIEGO: ACADEMIC PRESS INC ELSEVIER SCIENCE, 2013, roč. 64, č. 1, s. 3-11. ISSN 1046-2023. Dostupné z: https://dx.doi.org/10.1016/j.ymeth.2013.05.025.

HAVRILA, Marek, Kamila RÉBLOVÁ, C. ZIRBEL, Neocles B. LEONTIS a Jiří ŠPONER. Isosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin-Ricin Internal Loop. Journal of Physical Chemistry B. New York: American Chemical Society, 2013, roč. 117, č. 46, s. 14302-14319. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp408530w.

ŠPONER, Jiří, Judit ŠPONEROVÁ, Arnošt MLÁDEK, Petr JURECKA, Pavel BANÁŠ a Michal OTYEPKA. Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment. Biopolymers. Hoboken: WILEY-BLACKWELL, 2013, roč. 99, č. 12, s. 978-988. ISSN 0006-3525. Dostupné z: https://dx.doi.org/10.1002/bip.22322.

SZABLA, Rafal Kazimierz, Deniz TUNA, Robert W GORA, Jiří ŠPONER, Andrzej L SOBOLEWSKI a Wolfgang DOMCKE. Photochemistry of 2-Aminooxazole, a Hypothetical Prebiotic Precursor of RNA Nucleotides. Journal of Physical Chemistry Letters. Washington: American Chemical Society, 2013, roč. 4, č. 16, s. 2785-2788. ISSN 1948-7185. Dostupné z: https://dx.doi.org/10.1021/jz401315e.

ŠPONER, Jiří, Arnošt MLÁDEK, Naděžda ŠPAČKOVÁ, Xiaohui H. CANG, Thomas E. CHEATHAM a Stefan GRIMME. Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations. Journal of the American Chemical Society. WASHINGTON: American Chemical Society, 2013, roč. 135, č. 26, s. 9785-9796. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/ja402525c.

PINO, Samanta, Giovanna COSTANZO, Alessandra GIORGI, Jiří ŠPONER, Judit ŠPONEROVÁ a Ernesto DI MAURO. Ribozyme Activity of RNA Nonenzymatically Polymerized from 3 ',5 '-Cyclic GMP. Entropy. Basel: MDPI AG, 2013, roč. 15, č. 12, s. 5362-5383. ISSN 1099-4300. Dostupné z: https://dx.doi.org/10.3390/e15125362.

ŠPONEROVÁ, Judit, Arnošt MLÁDEK a Jiří ŠPONER. Structural and energetic factors controlling the enantioselectivity of dinucleotide formation under prebiotic conditions. Physical Chemistry Chemical Physics. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2013, roč. 15, č. 17, s. 6235-6242. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c3cp44156c.

STADLBAUER, Petr, Miroslav KREPL, Thomas E. CHEATHAM, Jaroslav KOČA a Jiří ŠPONER. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Research. Oxford, UK: Oxford Press, 2013, roč. 41, č. 14, s. 7128-7143. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkt412.

DRŠATA, Tomáš, Alberto PEREZ, Modesto OROZCO, Alexandre V MOROZOV, Jiří ŠPONER a Filip LANKAŠ. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2013, roč. 9, č. 1, s. 707-721. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct300671y.

SZABLA, Rafal Kazimierz, Judit ŠPONEROVÁ, Jiří ŠPONER a Robert W. GORA. Theoretical studies of the mechanism of 2-aminooxazole formation under prebiotically plausible conditions. Physical Chemistry Chemical Physics. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2013, roč. 15, č. 20, s. 7812-7818. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c3cp50320h.

ZGARBOVA, Marie, Javier F. LUQUE, Jiří ŠPONER, Thomas E III CHEATHAM, Michal OTYEPKA a Petr JUREČKA. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2013, roč. 9, č. 5, s. 2339-2354. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct400154j.

ZGARBOVÁ, Marie, F. JAVIER LUQUE, Jiří ŠPONER, Michal OTYEPKA a Petr JUREČKA. A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2012, roč. 8, č. 9, s. 3232-3242. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct3001987.

BANÁŠ, Pavel, Arnošt MLÁDEK, Michal OTYEPKA, Marie ZGARBOVA, Petr JURECKA, Daniel SVOZIL, Filip LANKAŠ a Jiří ŠPONER. Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2012, roč. 8, č. 7, s. 2448-2460. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct3001238.

ŠPONER, Jiří, Claudio A MORGADO a Daniel SVOZIL. Comment on "Computational Model for Predicting Experimental RNA and DNA Nearest-Neighbor Free Energy Rankings". Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2012, roč. 116, č. 28, s. 8331-8332. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp300659f.

ŠPONEROVÁ, Judit, Arnošt MLÁDEK, Jiří ŠPONER a Miguel FUENTES-CABRERA. Formamide-Based Prebiotic Synthesis of Nucleobases: A Kinetically Accessible Reaction Route. The Journal of Physical Chemistry A. Washington: American Chemical Society, 2012, roč. 116, č. 1, s. 720-726. ISSN 1089-5639. Dostupné z: https://dx.doi.org/10.1021/jp209886b.

OVAERE, Margriet, Jiří ŠPONER, Judit ŠPONEROVÁ, Piet HERDEWIJN a Luc VAN MEERVELT. How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid: ribonucleic acid duplex. Nucleic Acids Research. Oxford, UK: Oxford Press, 2012, roč. 40, č. 15, s. 7573-7583. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gks470.

FONVILLE, Judith M, Marcel SWART, Zuzana VOKACOVA, Vladimir SYCHROVSKY, Judit ŠPONEROVÁ, Jiří ŠPONER, Cornelis W HILBERS, F Matthias BICKELHAUPT a Sybren S WIJMENGA. Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment. Chemistry - A European Journal. WEINHEIM: WILEY-VCH, 2012, roč. 18, č. 39, s. 12372-12387. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201103593.

ŠPONEROVÁ, Judit a Jiří ŠPONER. Is formamide nature’s choice to create life? Comment on the paper “Formamide and the origin of life” by Raffaele Saladino et al. PHYSICS OF LIFE REVIEWS. Amserdam: Elsevier, 2012, roč. 9, č. 1, s. 109-110. ISSN 1571-0645. Dostupné z: https://dx.doi.org/10.1016/j.plrev.2011.12.015.

ŠPONER, Jiří, Xiaohui CANG a Thomas E CHEATHAM. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods. SAN DIEGO: ACADEMIC PRESS INC ELSEVIER SCIENCE, 2012, roč. 57, č. 1, s. 25-39. ISSN 1046-2023. Dostupné z: https://dx.doi.org/10.1016/j.ymeth.2012.04.005.

ŠPONER, Jiří, Michal OTYEPKA, Pavel BANÁŠ, Kamila RÉBLOVÁ a Nils WALTER. Molecular Dynamics Simulations of RNA Molecules. In Tamar Schlick. Innovations in Biomolecular Modeling and Simulations. 1. vydání. Cambridge: The Royal Society of Chemistry, 2012, s. 129-155. Volume 2. ISBN 978-1-84973-462-2.

BANÁŠ, Pavel, Petr SKLENOVSKY, Joseph E WEDEKIND, Jiří ŠPONER a Michal OTYEPKA. Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2012, roč. 116, č. 42, s. 12721-12734. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp309230v.

FERUS, Martin, Svatopluk CIVIS, Arnošt MLÁDEK, Jiří ŠPONER, Libor JUHA a Judit ŠPONEROVÁ. On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event. Journal of the American Chemical Society. WASHINGTON: American Chemical Society, 2012, roč. 134, č. 51, s. 20788-20796. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/ja310421z.

KREPL, Miroslav, Marie ZGARBOVA, Petr STADLBAUER, Michal OTYEPKA, Pavel BANÁŠ, Jaroslav KOČA, Thomas E. CHEATHAM, Petr JURECKA a Jiří ŠPONER. Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2012, roč. 8, č. 7, s. 2506-2520. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct300275s.

BEŠŠEOVÁ, Ivana, Pavel BANÁŠ, Petra KUEHROVA, Pavlina KOSINOVA, Michal OTYEPKA a Jiří ŠPONER. Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. Journal of Physical Chemistry B. WASHINGTON: American Chemical Society, 2012, roč. 116, č. 33, s. 9899-9916. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp3014817.

RÉBLOVÁ, Kamila, Jiří ŠPONER a Filip LANKAŠ. Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Research. Oxford, UK: Oxford Press, 2012, roč. 40, č. 13, s. 6290-6303. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gks258.

ŠPONER, Jiří, Arnošt MLÁDEK, Judit ŠPONEROVÁ, Daniel SVOZIL, Marie ZGARBOVÁ, Pavel BANÁŠ, Petr JUREČKA a Michal OTYEPKA. The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. PHYSICAL CHEMISTRY CHEMICAL PHYSICS. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2012, roč. 14, č. 44, s. 15257-15277. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c2cp41987d.

MORGADO, Claudio A, Daniel SVOZIL, Douglas H TURNER a Jiří ŠPONER. Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes. Physical Chemistry Chemical Physics. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2012, roč. 14, č. 36, s. 12580-12591. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c2cp40556c.

MLÁDEK, Arnošt, Judit ŠPONEROVÁ, Petr KULHÁNEK, Xiang-Jun LU, Wilma K. OLSON a Jiří ŠPONER. Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. Journal of Chemical Theory and Computation. Washington: ACS, 2012, roč. 8, č. 1, s. 335-347. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct200712b.

RÉBLOVÁ, Kamila, Judit ŠPONEROVÁ, Naděžda ŠPAČKOVÁ, Ivana BEŠŠEOVÁ a Jiří ŠPONER. A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis. JOURNAL OF PHYSICAL CHEMISTRY B. Washington: American Chemical Society, 2011, roč. 115, č. 47, s. 13897-13910. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp2065584.

FIALA, Radovan, Naděžda ŠPAČKOVÁ, Silvie FOLDYNOVÁ-TRANTÍRKOVÁ, Jiří ŠPONER, Vladimír SKLENÁŘ a Lukáš TRANTÍREK. NMR cross-­correlated relaxation rates reveal ion coordination sites in DNA. Journal of the American Chemical Society. Washington, DC., USA: American Chemical Society, 2011, roč. 133, č. 35, s. 13790-13793. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/ja202397p.

ZGARBOVA, Marie, Petr JUREČKA, Pavel BANÁŠ, Michal OTYEPKA, Judit ŠPONEROVÁ, Neocles B. LEONTIS, Craig L. ZIRBEL a Jiří ŠPONER. Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base-Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations. JOURNAL OF PHYSICAL CHEMISTRY A. Washington: American Chemical Society, 2011, roč. 115, č. 41, s. 11277-11292. ISSN 1089-5639. Dostupné z: https://dx.doi.org/10.1021/jp204820b.

MLÝNSKÝ, Vojtěch, Pavel BANÁŠ, Nils G. WALTER, Jiří ŠPONER a Michal OTYEPKA. QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms. JOURNAL OF PHYSICAL CHEMISTRY B. Washington: American Chemical Society, 2011, roč. 115, č. 47, s. 13911-13924. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp206963g.

RÉBLOVÁ, Kamila, Zora STŘELCOVÁ, Petr KULHÁNEK, Ivana BEŠŠEOVÁ, David H. MATHEWS, Keith VAN NOSTRAND, Ilyas YILDIRIM, Douglas H. TURNER a Jiří ŠPONER. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods. Journal of Chemical Theory and Computation. 2010, roč. 2010, č. 6, s. 910-929, 19 s. ISSN 1549-9618.

MLÁDEK, Arnošt, Judit ŠPONEROVÁ, Petr JUREČKA, Pavel BANÁŠ, Michal OTYEPKA, Daniel SVOZIL a Jiří ŠPONER. Conformational Energies of DNA Sugar Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. Journal of Chemical Theory and Computation. 2010, roč. 6/2010, č. 12, s. 3817-3835. ISSN 1549-9618.

RÉBLOVÁ, Kamila, Filip RÁZGA, Wen LI, Haixiao GAO, Joachim FRANK a Jiří ŠPONER. Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Nucleic Acids Research. 2010, roč. 38, č. 4, 16 s. ISSN 0305-1048.

BEŠŠEOVÁ, Ivana, Kamila REBLOVA, Leontis NEOCLES a Jiri SPONER. Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Research. Wiley InterScience, 2010, roč. 38, č. 18, s. 732-746, 19 s. ISSN 0305-1048.

SHARMA, Purshotam, Judit SPONER, Jiří ŠPONER, Sitansh SHARMA, Dhananjay BHATTACHARYYA a Abhijit MITRA. On the Role of the cis Hoogsteen:Sugar-Edge Family of Base Pairs in Platforms and Triplets: Quantum Chemical Insights into RNA Structural Biology. Jouranl of Physical Chemistry B. 2010, roč. 114, -, 14 s. ISSN 1520-6106.

MORGADO, Claudio, Petr JUREČKA, Daniel SVOZIL, pavel HOBZA a Jiří ŠPONER. Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Physical Chemistry Chemical Physics. 2010, roč. 14, -, s. 3522-3534. ISSN 1463-9076.

ŠPAČKOVÁ, Naděžda, Kamila RÉBLOVÁ a Jiri SPONER. Structural Dynamics of the Box C/D RNA Kink-Turn and Its Complex with Proteins: The Role of the A-Minor 0 Interaction, Long-Residency Water Bridges, and Structural Ion-Binding Sites Revealed by Molecular Simulations. Jouranl of Physical Chemistry B. 2010, roč. 114, č. 32, 13 s. ISSN 1520-6106.

ŠPONER, Judit, Alvaro VAZQUEZ-MAYAGOITIA, Bobby SUMPTER, Jerzy LESZCZYNSKI, Jiří ŠPONER, Michal OTYEPKA, Pavel BANÁŠ a Miguel FUENTES-CABRERA. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. Chemistry – A European Journal. 2010, roč. 16, č. 10, s. 3057-3065. ISSN 0947-6539.

MORGADO, Claudio, Petr JUREČKA, Daniel SVOZIL, Pavel HOBZA a Jiří ŠPONER. Balance of Attraction and Repulsion in Nucleic Acid Base Stacking: CCSD(T)/Complete Basis Set Limit Calculations on Uracil Dimer and a Comparison with the Force Field Description. Journal of Chemical Theory and Computation. 2009, roč. 5, č. 1, s. 1524-1544. ISSN 1549-9618.

ZIRBEL, Craig, Judit ŠPONER, Jiří ŠPONER, Jesse STOMBAUGH a Neocles LEONTIS. Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Research. Oxford University Press, 2009, roč. 37, č. 15, s. 4898 - 4918. ISSN 0305-1048.

BEŠŠEOVÁ, Ivana, Michal OTYEPKA, Kamila RÉBLOVÁ a Jiří ŠPONER. Dependence of A-RNA simulations on the choice of the force field and salt strength. Physical Chemistry Chemical Physics. 2009, roč. 11, -, s. 10701-10711. ISSN 1463-9076.

YILDIRIM, Ilyas, Harry STERN, Jiří ŠPONER, Naděžda ŠPAČKOVÁ a Douglas TURNER. Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCIG Base Pairs. Journal of Chemical Theory and Computation. 2009, roč. 5, č. 8, s. 2088–2100. ISSN 1549-9618.

ŠPONER, Jiří, Marie ZGARBOVÁ, Petr JUREČKA, Kevin RILEY, Judit ŠPONER a Pavel HOBZA. Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2OH Group of Ribose. Journal of Chemical Theory and Computation. 2009, roč. 5, č. 4, s. 1166–1179. ISSN 1549-9618.

SYCHROVSKÝ, Vladimír, Silvie FOLDÝNOVÁ-TRANTÍRKOVÁ, Naděžda ŠPAČKOVÁ, Koen ROBEYNS, Luc VAN MEERVELT, Wulf BLANKENFELDT, Zuzana VOKÁČOVÁ, Jiří ŠPONER a Lukáš TRANTÍREK. Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion. Nucleic Acids Research. Oxford University Press, 2009, roč. 37, č. 21, s. 7321-7331. ISSN 0305-1048.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Sarzynska JOANNA, Jaroslav KOČA, Modesto OROZCO, Thomas CHEATHAM, Tadeusz KULINSKI a Jiri SPONER. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. Journal of Chemical Theory and Computation. 2009, roč. 5, č. 9, s. 2514-2530. ISSN 1549-9618.

MLÁDEK, Arnošt, Purshotam SHARMA, Abhijit MITRA, Dhananjay BHATTACHARYYA, Jiří ŠPONER a Judit ŠPONER. Trans Hoogsteen/Sugar Edge Base Pairing in RNA. Structures, Energies, and Stabilities from Quantum Chemical Calculations. Journal of Physical Chemistry B. 2009, roč. 113, č. 6, s. 1743–1755. ISSN 1520-6106.

SARZYNSKA, Joanna, Kamila REBLOVA, Jiri SPONER a Tadeusz KULINSKI. Conformational Transitions of Flanking Purines in HIV-1 RNA Dimerization Initiation Site Kissing Complexes Studied by Charmm Explicit Solvent Molecular Dynamics. Biopolymers. Wiley InterScience, 2008, roč. 89, č. 9, s. 732-746, 13 s. ISSN 0006-3525.

BANAS, Pavel, Lubomir RULISEK, Veronika HANOSOVA, Daniel SVOZIL, Nils WALTER, Jiri SPONER a Michal OTYEPKA. General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility. Journal of Physical Chemistry B. 2008, roč. 112, č. 35, s. 11177–11187. ISSN 1520-6106.

SVOZIL, Daniel, Judit SPONER, Ivan MARCHAN, Alberto PEREZ, Thomas CHEATHAM, Ferda FORTI, Javier LUQUE, Modesto OROZCO a Jiri SPONER. Geometrical and Electronic Structure Variability of the Sugar-phosphate Backbone in Nucleic Acids. Journal of Physical Chemistry B. 2008, roč. 112, č. 27, s. 8188–8197. ISSN 1520-6106.

KOSENKOV, Dmytro, Leonid GORB, Oleg SHISHKIN, Jiri SPONER a Jerzy LESZCZYNSKI. Tautomeric Equilibrium, Stability, and Hydrogen Bonding in 2-Deoxyguanosine Monophosphate Complexed with Mg2+. JOURNAL OF PHYSICAL CHEMISTRY B. 2008, roč. 112, č. 1, s. 150-157. ISSN 1520-6106.

SPONER, Judit E, Bobby SUMPTER, Jerzy LESZCZYNSKI, Jiří ŠPONER a Miguel FUENTES-CABRERA. Theoretical Study on the Factors Controlling the Stability of the Borate Complexes of Ribose, Arabinose, Lyxose, and Xylose. Chemistry – A European Journal. Germany: Wiley, 2008, roč. 32/2008, č. 14, s. 9990-9998. ISSN 0947-6539.

ŠPONER, Jiří. Computational studies of nucleic acids, advances and failures. In Modeling Interactions in Biomolecules III. Praha: Mff UK, Praha, 2007, s. 51.

RÉBLOVÁ, Kamila, Eva FADRNÁ, Sarzynska JOANNA, Tadeusz KULINSKI, Petr KULHÁNEK, Eric ENNIFAR, Jaroslav KOČA a Jiri SPONER. Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by Molecular Dynamics. Biophysical Journal. New York, USA: Rockefeller University, 2007, roč. 93, č. 11, s. 3932-3949. ISSN 0006-3495.

RÁZGA, Filip, Jaroslav KOČA, Ali MOKDAD a Jiří ŠPONER. Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Research. Oxford, UK: Oxford Press, 2007, roč. 35, č. 12, s. 4007–4017. ISSN 0305-1048.

RÁZGA, Filip, Jaroslav KOČA a Jiří ŠPONER. Elastic properties of ribosomal RNA building blocks: Molecular dynamics study. In Strukturní biofyzika makromolekul II. první. Brno: Brno, 2007, s. 14-14.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Daniel SVOZIL, Jiří ŠPONER a Jaroslav KOČA. Human telomeric G-DNA - a test example for force field adjustment. In Journal Of Biomolecular Structure and Dynamics. Albany: Adenine Press, 2007, s. 709-709. ISSN 0006-3525.

ŠPONER, Jiří. Molecular dynamics simulations of quadruplex DNA. In First international meeting on quadruplex DNA,. Louisville, USA: Louisville, USA, 2007, s. 20.

MCDOWELL, Elizabeth, Naďa ŠPAČKOVÁ, Jiří ŠPONER a Nils WALTER. Molecular dynamics simulations of RNA: An in silico single molecule approach. BIOPOLYMERS. 2007, roč. 85, č. 2, s. 169-184. ISSN 0006-3525.

PEREZ, Alberto, Ivan MARCHAN, Daniel SVOZIL, Jiří ŠPONER, Thomas CHEATHAM a Charles LAUGHTON. Refinement of the AMBER force field for nucleic acids: Improving the description of alfa/gamma conformers. Biophysical Journal. 2007, roč. 92, č. 11, s. 3817-3829. ISSN 0006-3495.

ŠPONER, Jiří, Ali MOKDAD, Filip RÁZGA, Kamila RÉBLOVÁ a Naděžda ŠPAČKOVÁ. Ribosomal RNA motifs and segments have salient flexibilities. In Journal Of Biomolecular Structure and Dynamics. prve. Albany: Adenine Press, 2007, s. 632-633. ISSN 0006-3525.

MENENI, Srinivasa, Steven SHELL, Lan GAO, Petr JURECKA, Wang LEE, Jiri SPONER, Yue ZOU, Paul CHIARELLI a Bongsup CHO. Spectroscopic and Theoretical Insights into Sequence Effects of Aminofluorene-Induced Conformational Heterogeneity and Nucleotide Excision Repair. Biochemistry. 2007, roč. 46/2007, č. 40, s. 11263-11278. ISSN 0006-2960.

RÉBLOVÁ, Kamila, Filip LANKAS a Jiri SPONER. Study of structure, dynamics and local elasticity of 16S rRNA Helix 44 using molecular dynamics methods. In Journal Of Biomolecular Structure and Dynamics. prve. Albany: Adenine Press, 2007, s. 635-635. ISSN 0006-3525.

FUENTES-CABRERA, Miguel, Bobby SUMPTER, Judit SPONER, Jiri SPONER, Leon PETIT a Jack WELLS. Theoretical study on structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA. JOURNAL OF PHYSICAL CHEMISTRY B. 2007, roč. 111, č. 4, s. 870-879. ISSN 1520-6106.

KRASOVSKA, Maryna, Jana SEVCIKOVA, Kamila REBLOVA, Bohdan SCHNEIDER, Walter NILS a Jiri SPONER. Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme. Biophysical Journal. USA: Biophysical Society, 2006, roč. 91, -, s. 626-638, 16 s. ISSN 0006-3495.

ŠPONER, Jiří a Filip LANKAŠ. Challenges and advances in computational chemistry and physics. Computational studies of RNA and DNA. Netherlands: Springer, 2006, 635 s. Volume 2. ISBN 1-4020-4794-0.

SPONER, Judit E, Jerzy LESZCZYNSKI a Jiří ŠPONER. Mechanism of action of anticancer titanocene derivatives: an insight from quantum chemical calculations. Journal of Physical Chemistry B. USA: The American Chemical Society, 2006, roč. 110/2006, č. 39, s. 19632-19636. ISSN 1089-5639.

ŠPAČKOVÁ, Naděžda, Thomas E CHEATHAM a Jiří ŠPONER. Molecular dynamics simulations of nucleic acids: MD simulations of G-DNA and functional RNAs. In Challenges and advances in computational chemistry and physics. Computational studies of RNA and DNA. Netherlands: Springer, 2006, s. 301-326. Volume 2. ISBN 1-4020-4794-0.

ŠPAČKOVÁ, Naděžda a Jiří ŠPONER. Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Research. Oxford University Press, 2006, roč. 34, č. 2, s. 697-708. ISSN 0006-3465.

ŠPONER, Jiří. Molecular interactions in nucleic acids. In Senior research fellows' meeting. London: Wellcome trust, 2006, s. 127-127.

SVOZIL, Dan, Jiří ŠPONER, Thomas E CHEATHAM a Modesto OROZCO. On the problem with long MD simulations of nucleic acids. In 2006 ISQBP president's meeting. Strasbourg: Strasbourg, 2006, s. 42-42.

ŠPONER, Jiří. Ribosom a syntéza bílkovin - fascinující molekulární LEGO. In 2006 Bioinformatika III, Invex. Brno: Brno, 2006, s. 1-1.

RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA a Jiří ŠPONER. RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics. Structure. USA: CELL PRESS, 1100 MASSACHUSETTS AVE, CAMB, 2006, roč. 14, č. 5, s. 825-835, 10 s. ISSN 0969-2126.

MOKDAD, Ali, Maryna KRASOVSKA, Jiří ŠPONER a Neocles B. LEONTIS. Structural and evolutionary classification of G/U wobble basepairs in the ribosome. Nucleic Acids Research. Oxford University Press, 2006, roč. 34, č. 5, s. 1326-1341. ISSN 0006-3465.

ŠPONER, Jiří. Structure and dynamics of functional RNAs: 3 microseconds of explicit solvent MD. In 2006 ISQBP president's meeting. Strasbourg: Strasbourg, 2006, s. 41-41.

ŠPONER, Jiří. Structure and dynamics of ribosomal RNA: The role of molecular interactions. In 2006 IBBI. Praha: Praha, 2006, s. 1-1.

ŠPONER, Jiří. Structure and dynamics of RNA and DNA. Advanced computational studies. In Materials Structure in chemistry, biology, physics and technology. Praha: Krystalografická společnost, 2006, s. 14. ISBN 1211-5894.

RÉBLOVÁ, Kamila, Filip LANKAŠ, Filip RÁZGA, Maryna V KRASOVSKA, Jaroslav KOČA a Jiří ŠPONER. Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations. Biopolymers. USA: Wiley InterScience, 2006, roč. 82, č. 5, s. 504-520. ISSN 0006-3525.

RHODES, Maria, Kamila REBLOVA, Walter NILS a Jiri SPONER. Trapped water molecules are essential to structural dynamics and function of a ribozyme. The Proceedings of the National Academy of Sciences. USA: National Academy of Sciences of the USA, 2006, roč. 103, č. 36, s. 13380-13385. ISSN 1091-6490.

RÁZGA, Filip, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Elbow-like motions in Ribosomal Kink-turns: The role of the second A-minor motif and Nominally unpaired bases. In Journal Of Biomolecular Structure and Dynamics. prve. New York, USA: Adenine Press, 2005, s. 800-801. ISBN 1533-0346.

RÁZGA, Filip, Jaroslav KOČA, Jiří ŠPONER a Neocles B. LEONTIS. Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases. Biophysical Journal. USA: Biophysical Society, 2005, roč. 88, č. 5, s. 3466-3485. ISSN 0006-3495.

FADRNÁ, Eva, Jaroslav KOČA a Jiří ŠPONER. Influence of Ion Parameters On Molecular Dynamics and/or Free Energy Calculation. In Workshop on Modelling interactions in Biomolecules II. Praha: Karlova Univerzita Praha, 2005, s. O, 1 s.

ŠPONER, Judit E, Naděžda ŠPAČKOVÁ, Petr KULHÁNEK, Jerzy LESZCZYNSKI a Jiří ŠPONER. Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. JOURNAL OF PHYSICAL CHEMISTRY A. 2005, roč. 109, č. 10, s. 2292-2301. ISSN 1089-5639.

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Ribosomal RNA Kink-turn motif - a flexible molecular hinge. In Materials Structure in chemistry, biology, physics and technology. prve. Praha: Krystalograficka spolecnost, 2005, s. 38-38. ISBN 1221-5894.

RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA a Jiří ŠPONER. RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function. In Strukturní biofyzika makromolekul. prvé. Brno: Biofyzikálny ústav AVČR a MU v Brne, 2005, s. 17-17.

RÁZGA, Filip, Jaroslav KOČA, N.B. LEONTIS a Jiří ŠPONER. RNA Kink-turns as Flexible Molecular Hinges of the Ribosomal "LEGO". The Role of Second A-minor Motif and Nominally Unpaired Bases. In 14th Conference on Current Trends in Computational Chemistry 2005. prvé. Jackson, Miss, USA: Jackson, Miss, USA, 2005, s. 126-126.

RÁZGA, Filip, Jaroslav KOČA, Neocles B LEONTIS a Jiří ŠPONER. RNA K-turns-Flexible Ribosomal Motifs:Dynamics, Hydration, Conformations and Biological Relevance. In Workshop on Modeling Interactions in Biomolecules II. prve. Praha: Praha, 2005, s. p37, 2 s.

RÉBLOVÁ, Kamila, Nadezda SPACKOVÁ, Jaroslav KOČA, Neocles LEONTIS a Jiri SPONER. Long-residency hydration, cation binding and dynamics of Loop E/Helix IV rRNA - L25 protein complex. Biophysical Journal. New York, USA: Rockefeller University, 2004, roč. 87, č. 5, s. 3397-3412. ISSN 0006-3465.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Jaroslav KOČA, Thomas E. CHEATHAM a Jiří ŠPONER. Molecular dynamics simulations of guanine quadruplex loops:Advances and force field limitations. Biophysical Journal. Bethesda, USA: Biophysical Society, 2004, roč. 87, č. 1, s. 227-242. ISSN 0006-3495.

RÁZGA, Filip, Jaroslav KOČA, Jiří ŠPONER a Neocles B. LEONTIS. Molekulově Dynamická simulace flexibilních RNA motivů. In Sborník abstraktů Studentská vědecká konference v oboru chemie a biochemie. 1. vyd. Brno: Přírodovědecká fakulta Masarykovy Univerzity v Brně Chemická sekce, 2004, s. 42.

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Ribosomal RNA Kink-turn motif - a flexible molecular hinge. In Conference on Current Trends in Computational Chemistry. prve. Jackson, MS, USA: Jackson, Miss, USA, 2004, s. 87-87.

RÁZGA, Filip, Naďa ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Ribosomal RNA Kink-turn Motif - A Flexible Molecular Hinge. Journal of Biomolecular Structure & Dynamics. Adenine Press, 2004, roč. 22, č. 2, s. 183-193. ISSN 0739-1102.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA. Conformational Flexibility of DNA sequences studied by Advanced Molecular Mechanics and Dynamics Tools. In Book of Abstracts. 2003. vyd. Praha: Workshop on Modeling Interactions in Biomolecules, 2003, s. 20.

ŠTEFL, Richard, Thomas E. CHEATHAM, Naděžda ŠPAČKOVÁ, Eva FADRNÁ, Imre BERGER, Jaroslav KOČA a Jiří ŠPONER. Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamics Analysis of the Substates. Biophysical Journal. Bethesda, USA: Biophysical Society, 2003, roč. 85, č. 3, s. 1787-1804. ISSN 0006-3495.

ŠPAČKOVÁ, Naděžda, Richard ŠTEFL, Imre BERGER, Eva FADRNÁ, Jaroslav KOČA, T.E. CHEATHAM III a Jiří ŠPONER. Molecular Dynamics of Guanine Quadruplex Molecules. In Book of Abstracts. Albany, NY, USA: 13th Conversatin in the Discipline Biomolecular Structure and Dynamics, 2003, s. 001-1.

RÉBLOVÁ, Kamila, Naděžda ŠPAČKOVÁ, Judit ŠPONER, Jaroslav KOČA a Jiři ŠPONER. Molecular dynamics simulations of RNA kissing loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Research. Oxford University Press, 2003, roč. 31, č. 23, s. 6942-6952. ISSN 0006-3465.

RÉBLOVÁ, Kamila, Naděžda ŠPAČKOVÁ, Jaroslav KOČA, Neocles LEONTIS a Jiří ŠPONER. Non-Watson-Crick Base Pairing and Hydration in RNA motifs: Molecular Dynamics of 5S rRNA Loop E. In Journal of Biomolecular Structure and Dynamics. Schenectady, New York 12304 USA: Adenine Press, 2003, s. 896-896.

RÉBLOVÁ, Kamila, Nadezda SPACKOVÁ, Richard STEFL, Kristina CSASZAR, Jaroslav KOCA, Neocles LEONTIS a Jiri SPONER. Non-Watson-Crick Basepairing and Hydration in RNA Motifs:. Biophysical Journal. New York, USA: Rockefeller University, 2003, roč. 84, č. 6, s. 3564-3582, 18 s. ISSN 0006-3465.

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Jiří ŠPONER a Neocles, B. LEONTIS. Structure and Dynamics of RNA K-turn Motifs. In RNA klub. vyd. Praha: Praha, 2003, s. 21-21.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA. Computer modelling of DNA quadruplex conformational behavior. In Chemické Listy. 2002. vyd. Praha: 54. Sjezd chemických společností, 2002, s. 425-426.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA. DNA quadruplexes with lateral loops - molecular modelling study of conformational behavior. In Chemometrics VI. 2002. vyd. Brno: Chemometrics VI, 2002, s. O17, 1 s. ISBN 80-210-2918-8.

RÉBLOVÁ, Kamila, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Kristina CSASZAR, Jaroslav KOČA, Neocles LEONTIS a Jiří ŠPONER. Molecular dynamics of the 5S rRNA loop E. In Chemometrics. Brno: Chemometrics VI., 2002, s. 18-18.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA. Molecular modelling of DNA fragment conformational behavior. In WATOC 02. 2002. vyd. Lugano, Švýcarsko: WATOC'02, 2002, s. PC438, 1 s.

ŠTEFL, Richard, Naděžda ŠPAČKOVÁ, Imre BERGER, Jaroslav KOČA a Jiří ŠPONER. Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. Biophysical Journal. Bethesda, USA: Biophysical Society, 2001, roč. 80, č. 1, s. 455-468. ISSN 0006-3495.

CSASZAR, Kristina, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Jiří ŠPONER a Neocles B. LEONTIS. Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non- Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding. Journal of Molecular Biology. London: Academic Press, 2001, roč. 313, č. 5, s. 1073-1091. ISSN 0022-2836.

DORNBERGER, Utz, Naděžda ŠPAČKOVÁ, Axel WALTER, Friedrich A. GOLLMICK, Jiří ŠPONER a hartmut FRITZSCHE. Solution structure of the dodecamer d-(CATGGGCC-CATG)(2) is B-DNA. Experimental and molecular dynamics study. Journal of Biomolecular Structure and Dynamics. GUILDERLAND: Adenine Press, 2001, roč. 19, č. 1, s. 159-174. ISSN 0739-1102.

ŠPAČKOVÁ, Naděžda, Imre BERGER a Jiří ŠPONER. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2001, roč. 123, č. 14, s. 3295-3307. ISSN 0002-7863.

ŠPAČKOVÁ, Naděžda, Imre BERGER a Jiří ŠPONER. Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules. The Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 1999, roč. 121, č. 23, s. 5519-5534. ISSN 0002-7863.

ŠPAČKOVÁ, Naděžda, Imre BERGER, Martin EGLI a Jiří ŠPONER. Molecular dynamics of hemiprotonated intercalated four-stranded i-DNA: stable trajectories on a nanosecond scale. The Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 1998, roč. 120, č. 24, s. 6147-6151. ISSN 0002-7863.