prof. RNDr. Jiří Šponer, DrSc.
Tel: 58 563 4760, E-mail: jiri.sponer@upol.cz, Room: 3.006
Research interests- Structural molecular biology and biophysics,
- physical chemistry of molecular interactions,
- computational chemistry,
- atomistic simulations of biopolymers,
- structural studies of functional RNA molecules (ribosome, ribozymes),
- DNA and their complexes with ligands and proteins,
- quantum-chemical studies of molecular interactions in nucleic acids,
- bioinformatics of nucleic acids.
- 1987 - Master degree (RNDr), Physics, Faculty of Science, MU Brno
- 1992 - CSc (eq. PhD), Biophysics, Faculty of Science, MU Brno
- 2001 - D.Sc. (Doctor of Science), Biophysics/Molecular Biology, Academy of Sciences of the Czech Republic
- 2002 - Associate Professor of Biophysics, Masaryk University, Brno
- 2009 - Professor of Biomolecular Chemistry, Masaryk University, Brno
- 1988-1989: Scholarship, Masaryk University, Faculty of Science, Brno (including one-year army service)
- 1990 - 1992: Postgraduate student, Masaryk University, Brno
- 1993: Scholarship, Institute of Biohysics, Academy of Sciences of the Czech Republic
- 1994-2003: Researcher and Senior Research, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic (part time 2001-2003)
- Since 2001: Senior Researcher and Head of Department, Institute of Biophysics, Academy of Sciences, Brno
- 2004-2011 (part time): Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Since 2007 (part time): Professor, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc.)
- Since 2011 (part time): Group leader and Professor, CEITEC and NCBR, MU, Brno
- Department of Chemistry, Jackson State University, Jackson, MS, USA. 1994 -2001, ca 15 months
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA 1997 - 2 weeks, 1998 - 2 weeks, 1999 - 2 weeks
- Department of Chemistry, University of Dortmund, Dortmund, Germany, 1999 - 3 weeks, 2000 - 3 weeks
- Department of Chemistry, Bowling Green State University, Bowling Green, OH, US, 2000, 2 weeks
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, USA, 2000, 1 week
- University Autonoma Barcelona, Barcelona, Spain, 2002, 1 month
- University of Sciences in Philadelphia, Philadelphia, USA, 2011, 2 weeks
Publications
2020
- Mlýnský V, Kührová P, Kühr T, Otyepka M, Bussi G, Banáš P, Šponer J: Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides. J. Chem. Theory Comput., 16(6), 3936-3946, 2020. (DOI)
- Šponer JE, Mohammadi E, Petera L, Saeidfirozeh H, Knížek A, Kubelík P, Krůs M, Juha L, Civiš S, Coulon R, Malina O, Ugolotti J, Ranc Václav , Otyepka M, Šponer J, Ferus M, Dudzak R: Formic acid, a ubiquitous but overlooked component of the early Earth atmosphere. Chem. Eur. J., 26(52), 12075-12080, 2020. (DOI)
2019
- Bochicchio A, Krepl M, Yanf F, Varani G, Šponer J, Carloni P: Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study. PLoS Comput. Biol., ASAP, 2019. (DOI)
- Cesari A, Bottaro S, Lindorfr-Larsen K, Banáš P, Šponer J, Bussi G: Fitting Corrections to an RNA Force Field Using Experimental Data. J. Chem. Theory Comput., 15(6), 3425-3431, 2019. (DOI)
- Gorecka KM, Krepl M, Szlachcic A, Poznanski J, Šponer J, Nowotny M: RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution. Nat. Commun., 10, 4102, 2019. (DOI)
- Kruse H, Banáš P, Šponer J: Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects. J. Chem. Theory Comput., 15(1), 95–115, 2019. (DOI)
- Kührová P, Mlýnský V, Zgarbová M, Krepl M, Bussi G, Best RB, Otyepka M, Šponer J, Banáš P: Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. J. Chem. Theory Comput., 15(5), 3288-3305, 2019. (DOI)
- Ripin N, Boudet J, Duszczyk MM, Hinniger A, Faller M, Krepl M, Gadi A, Schneider RJ, Šponer J, Meisner-Kober NC, Allain FH-: Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM. Proc. Natl. Acad. Sci. U.S.A, 116(8), 2935-2944, 2019. (DOI)
- Šponer JE, Šponer J, Di Mauro E: Structural and Energetic Compatibility: The Driving Principles of Molecular Evolution. Astrobiol, 19(9), 1117-1122, 2019. (DOI)
- Stadlbauer P, Kührová P, Vicherek L, Banáš P, Otyepka M, Trantírek L, Šponer J: Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. Nucleic Acids Res., 47(14), 7276–7293, 2019. (DOI)
- Suddala KC, Price IR, Dandpat SS, Janeček M, Kührová P, Šponer J, Banáš P, Ke A, Walter NG: Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch. Nat. Commun., 10, 4304, 2019. (DOI)
2018
- Cassone G, Šponer J, Šponer JE, Pietrucci F, Saitta AM, Saija F: Synthesis of (D)-erythrose from glycolaldehyde aqueous solutions under electric field. Chem. Commun., 54, 3211-3214 , 2018. (DOI)
- Figiel M, Krepl M, Park S, Poznański J, Skowronek,Krzysztof , Gołąb A, Ha T, Šponer J, Nowotny M: Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase. J. Biol. Chem., 293, 191-202, 2018. (DOI)
- Havrila M, Stadlbauer P, Kührová P, Banáš P, Mergny J, Otyepka M, Šponer J: Structural dynamics of propeller loop: towards folding of RNA G-quadruplex. Nucleic Acids Res., 46(17), 8754–8771, 2018. (DOI)
- Krepl M, Voegele J, Kruse H, Duchardt-Ferner E, Woehnert J, Šponer J: An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch. Nucleic Acids Res., 46(13), 6528-6543, 2018. (DOI)
- Li Q, Froning JP, Pykal M, Zhang S, Wang Z, Vondrák M, Banáš P, Čépe K, Jurečka P, Šponer J, Zbořil R, Dong M, Otyepka M: RNA nanopatterning on graphene. 2D Mater, 5, 031006, 2018. (DOI)
- Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Ley AG, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M: RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem. Rev., 118(8), 4177–4338, 2018. (DOI)
- Szabla R, Kruse H, Stadlbauer P, Šponer J, Sobolewski AL: Sequential electron transfer governs the UV-induced self-repair of DNA photolesions. Chem. Sci., 9(12), 3131-3140, 2018. (DOI)
- Zgarbová M, Jurečka P, Šponer J, Otyepka M: A- to B-DNA Transition in AMBER Force Fields and its Coupling to Sugar Pucker. J. Chem. Theory Comput., 14(1), 319–328, 2018. (DOI)
2017
- Cassone G, Šponer J, Saija F, Di Mauro E, Saitta AM, Šponer JE: Stability of 2’,3’ and 3’,5’ cyclic nucleotides in formamide and in water: a theoretical insight into the factors controlling accumulation of nucleic acid building blocks in the prebiotic pool. Phys. Chem. Chem. Phys., 19, 1817-1825, 2017. (DOI)
- Costanzo G, Giorgi A, Scipioni A, Timperio AM, Mancone C, Tripodi M, Kapralov M, Krasavin E, Kruse H, Šponer J, Šponer JE, Ranc Václav , Otyepka M, Pino S, Di Mauro E: Nonenzymatic Oligomerization of 3',5' Cyclic CMP Induced by Proton- and UV-Irradiation Hints at a Non-Fastidious Origin of RNA. ChemiBioChem, 18(5), 1535–1543, 2017. (DOI)
- Diarra dit Konté N, Krepl M, Damberger FF, Duss O, Šponer J, Allain FH: Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination. Nat. Commun., 8(654), 2017. (DOI)
- Figiel M, Krepl M, Poznaňaski J, Golab A, Šponer J, Nowotny M: Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase. Nucleic Acids Res., 45(6), 3341–3352, 2017. (DOI)
- Havrila M, Stadlbauer P, Islam B, Otyepka M, Šponer J: Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes. J. Chem. Theory Comput., 13(8), 3911–3926, 2017. (DOI)
- Islam B, Stadlbauer P, Ley AG, Pérez-Hernández G, Haider S, Neidle S, Bussi G, Banáš P, Otyepka M, Šponer J: Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. J. Chem. Theory Comput., 13(6), 2458–2480, 2017. (DOI)
- Krepl M, Blatter M, Cléry A, Damberger FF, Allain FH, Šponer J: Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition. Nucleic Acids Res., 45(13), 8046–8063, 2017. (DOI)
- Mlýnský V, Kührová P, Jurečka P, Šponer J, Otyepka M, Banáš P: Mapping the Chemical Space of the RNA Cleavage and its Implications for Ribozyme Catalysis. J. Phys. Chem. B, 121(48), 10828–10840, 2017. (DOI)
- Pokorná P, Krepl M, Kruse H, Šponer J: MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, L-histidine Ligand and Mg2+. J. Chem. Theory Comput., 13(11), 5658–5670, 2017. (DOI)
- Saladino R, Bizzarri BM, Botta L, Šponer J, Šponer JE, Georgelin T, Jaber M, Rigaud B, Kapralov M, Timoshenko GN, Rozanov A, Krasavin E, Timperio AM, Di Mauro E: Proton irradiation: a key to the challenge of N-glycosidic bond formation in a prebiotic context. Sci. Rep., 7, 14709, 2017. (DOI)
- Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M: Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochim. Biophys. Acta, Gen. Subj., 1861(5), 1246–1263, 2017. (DOI)
- Šponer J, Krepl M, Banáš P, Kührová P, Zgarbová M, Jurečka P, Havrila M, Otyepka M: How to understand atomistic molecular dynamics simulations of RNA and protein– RNA complexes? WIREs RNA, 8(3), e1405, 2017. (DOI)
- Zgarbová M, Jurečka P, Banáš P, Havrila M, Šponer J, Otyepka M: Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field. J. Phys. Chem. B, 121(11), 2420–2433, 2017. (DOI)
- Zgarbová M, Jurečka P, Lankaš F, Cheatham TE, Šponer J, Otyepka M: Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for all 136 Distinct Tetranucleotide Sequences. J. Chem. Inf. Model., 57(2), 275–287, 2017. (DOI)
2016
- Bottaro S, Banáš P, Šponer J, Bussi G: Free Energy Landscape of GAGA and UUCG RNA Tetraloops. J. Phys. Chem. Lett., 7, 4032–4038, 2016. (DOI)
- Dršata T, Zgarbová M, Jurečka P, Šponer J, Lankaš F: On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA. Biophys. J., 110(4), 874–876, 2016. (DOI)
- Galindo-Murillo R, Robertson JC, Zgarbová M, Šponer J, Otyepka M, Jurečka P, Cheatham TE: Assessing the current state of AMBER force field modifications for DNA. J. Chem. Theory Comput., 12(8), 4114–4127, 2016. (DOI)
- Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P: Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. J. Chem. Theory Comput., 12(9), 4534–4548, 2016. (DOI)
- Stadlbauer P, Mazzanti L, Cragnolini T, Wales DJ, Derreumaux P, Pasquali S, Šponer J: Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. J. Chem. Theory Comput., 12(12), 6077–6097, 2016. (DOI)
2015
- Dubecký M, Walter NG, Šponer J, Otyepka M, Banáš P: Chemical Feasibility of the General Acid / Base Mechanism of glmS Ribozyme Self-Cleavage. Biopolymers, 103(10), 550–562, 2015. (DOI)
- Estarellas C, Otyepka M, Koča J, Banáš P, Krepl M, Šponer J: Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochim. Biophys. Acta, Gen. Subj., 1850(5), 1072-1090, 2015. (DOI)
- Haldar S, Kührová P, Banáš P, Spiwok V, Šponer J, Hobza P, Otyepka M: Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics. J. Chem. Theory Comput., 11(8), 3866-3877, 2015. (DOI)
- Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J: 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. J. Phys. Chem. B, 119, 15176−15190, 2015. (DOI)
- Krepl M, Havrila M, Stadlbauer P, Banáš P, Otyepka M, Pasulka J, Štefl R, Šponer J: Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein–RNA Complexes?. J. Chem Theory Comput., 11(3), 1220-1243, 2015. (DOI)
- Mlýnský V, Kührová P, Zgarbová M, Jurečka P, Walter NG, Otyepka M, Šponer J, Banáš P: Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with $epsilon$/$zeta$ Force Field Reparametrizations. J. Phys. Chem. B., 119(11), 4220-4229, 2015. (DOI)
- Mlýnský V, Walter NG, Šponer J, Otyepka M, Banáš P: The role of an active site Mg 2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations. Phys. Chem. Chem. Phys., 17(1), 670-679, 2015. (DOI)
- Sripathi KN, Banáš P, Réblová K, Šponer J, Otyepka M, Walter NG: Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics. Phys. Chem. Chem. Phys., 17(8), 5887-5900, 2015. (DOI)
- Stadlbauer P, Kührová P, Banáš P, Koča J, Bussi G, Trantírek L, Otyepka M, Šponer J: Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic. Acids Res., 43(20), 9626-9644, 2015. (DOI)
- Zgarbová M, Šponer J, Otyepka M, Cheatham TE, Galindo-Murillo R, Jurečka P: Refinement of the Sugar-Phosphate Backbone Torsion Beta for the AMBER Force Fields Improves the Description of Z-DNA and B-DNA. J. Chem. Theory Comput., 11(12), 5723–5736, 2015. (DOI)
2014
- Dršata T, Špačková N, Jurečka P, Zgarbová M, Šponer J, Lankaš F: Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. Nucleic Acids Res., 42(11), 7383-7394, 2014. (DOI)
- Dršata T, Zgarbová M, Špačková N, Jurečka P, Šponer J, Lankaš F: Mechanical Model of DNA Allostery. J. Phys. Chem. Lett., 5(21), 3831-3835, 2014. (DOI)
- Kührová P, Otyepka M, Šponer J, Banáš P: Are Waters around RNA More than Just a Solvent? – An Insight from Molecular Dynamics Simulations. J. Chem. Theory Comput., 10(1), 401-411, 2014. (DOI)
- Mládek A, Banáš P, Jurečka P, Otyepka M, Zgarbová M, Šponer J: 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. J. Chem. Theory Comput., 10(1), 463-480, 2014. (DOI)
- Mlýnský V, Banáš P, Šponer J, van der Kamp MW, Mulholland AJ, Otyepka M: Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. J. Chem. Theory Comput., 10(4), 1608-1622, 2014. (DOI)
- Šponer J, Banáš P, Jurečka P, Zgarbová M, Kührová P, Havrila M, Krepl M, Stadlbauer P, Otyepka M: Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. J. Phys. Chem. Lett., 5(10), 1771-1782, 2014. (DOI)
- Sripathi KN, Tay WW, Banáš P, Otyepka M, Šponer J, Walter NG: Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. RNA, 20(7), 1112-1128, 2014. (DOI)
- Zgarbová M, Otyepka M, Šponer J, Lankaš F, Jurečka P: Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA. J. Chem. Theory Comput., 10(8), 3177-3189, 2014. (DOI)
2013
- Krepl M, Otyepka M, Banáš P, Šponer J: Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study. J. Phys. Chem. B, 117(6), 1872-1879, 2013. (DOI)
- Kührová P, Banáš P, Best RB, Šponer J, Otyepka M: Computer Folding of RNA Tetraloops? Are We There Yet?. J. Chem. Theory Comput., 9(4), 2115-2125, 2013. (DOI)
- Mládek A, Krepl M, Svozil D, Čech P, Otyepka M, Banáš P, Zgarbová M, Jurečka P, Šponer J: 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. Phys. Chem. Chem. Phys., 15(19), 7295-7310, 2013. (DOI)
- Šponer J, Šponer JE, Mládek A, Banáš P, Jurečka P, Otyepka M: How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods, 64(1), 3-11, 2013. (DOI)
- Šponer J, Šponer JE, Mládek A, Jurečka P, Banáš P, Otyepka M: Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment. Biopolymers, 99(12), 978–988, 2013. (DOI)
- Zgarbová M, Luque FJ, Šponer J, Cheatham TE, Otyepka M, Jurečka P: Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J. Chem. Theory Comput., 9(5), 2339-2354, 2013. (DOI)
2012
- Banáš P, Mládek A, Otyepka M, Zgarbová M, Jurečka P, Svozil D, Lankaš F, Šponer J: Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. J. Chem. Theory Comput., 8(7), 2448-2460, 2012. (DOI)
- Banáš P, Sklenovský P, Wedekind JE, Šponer J, Otyepka M: Molecular Mechanism of preQ 1 Riboswitch Action: A Molecular Dynamics Study. J. Phys. Chem. B, 116(42), 12721-12734, 2012. (DOI)
- Beššeová I, Banáš P, Kührová P, Košinová P, Otyepka M, Šponer J: Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. J. Phys. Chem. B, 116(33), 9899-9916, 2012. (DOI)
- Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, Koča J, Cheatham TE, Jurečka P, Šponer J: Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. J. Chem. Theory Comput., 8(7), 2506-2520, 2012. (DOI)
- Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M: The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys. Chem. Chem. Phys., 14(44), 15257-15277, 2012. (DOI)
- Šponer J, Otyepka M, Banáš P, Réblová K, Walter NG: Chapter 6. Molecular Dynamics Simulations of RNA Molecules. 129-155, 2012. (DOI)
- Zgarbová M, Luque FJ, Šponer J, Otyepka M, Jurečka P: A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects. J. Chem. Theory Comput., 8(9), 3232-3242, 2012. (DOI)
2011
- Mlýnský V, Banáš P, Walter NG, Šponer J, Otyepka M: QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms. J. Phys. Chem. B, 115(47), 13911-13924, 2011. (DOI)
- Sklenovský P, Florová P, Banáš P, Réblová K, Lankaš F, Otyepka M, Šponer J: Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs. J. Chem. Theory Comput., 7(9), 2963-2980, 2011. (DOI)
- Zgarbová M, Jurečka P, Banáš P, Otyepka M, Šponer JE, Leontis NB, Zirbel CL, Šponer J: 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. J. Phys. Chem. A, 115(41), 11277-11292, 2011. (DOI)
- Zgarbová M, Otyepka M, Šponer J, Mládek A, Banáš P, Cheatham TE, Jurečka P: Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 7(9), 2886-2902, 2011. (DOI)
2010
- Banáš P, Hollas D, Zgarbová M, Jurečka P, Orozco M, Cheatham TE, Šponer J, Otyepka M: Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. J. Chem. Theory Comput., 6(12), 3836-3849, 2010. (DOI)
- Banáš P, Walter NG, Šponer J, Otyepka M: Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics. J. Phys. Chem. B, 114(26), 8701-8712, 2010. (DOI)
- Mládek A, Šponer JE, Jurečka P, Banáš P, Otyepka M, Svozil D, Šponer J: Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. J. Chem. Theory Comput., 6(12), 3817-3835, 2010. (DOI)
- Mlýnský V, Banáš P, Hollas D, Réblová K, Walter NG, Šponer J, Otyepka M: Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H + Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme. J. Phys. Chem. B, 114(19), 6642-6652, 2010. (DOI)
- Morgado CA, Jurečka P, Svozil D, Hobza P, Šponer J: 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. Phys. Chem. Chem. Phys., 12(14), 3522-3534, 2010. (DOI)
- Šponer JE, Vázquez-Mayagoitia Á, Sumpter BG, Leszczynski J, Šponer J, Otyepka M, Banáš P, Fuentes-Cabrera M: Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. Chem. Eur. J., 16(10), 3057-3065, 2010. (DOI)
- Zgarbová M, Otyepka M, Šponer J, Hobza P, Jurečka P: Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys. Chem. Chem. Phys., 12(35), 10476-10493, 2010. (DOI)
2009
- Banáš P, Jurečka P, Walter NG, Šponer J, Otyepka M: Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. Methods, 49(2), 202-216, 2009. (DOI)
- Beššeová I, Otyepka M, Réblová K, Šponer J: Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys. Chem. Chem. Phys., 11(45), 10701-10711, 2009. (DOI)
- Morgado CA, Jurečka P, Svozil D, Hobza P, Šponer J: 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. J. Chem. Theory Comput., 5(6), 1524-1544, 2009. (DOI)
- Šponer J, Zgarbová M, Jurečka P, Riley KE, Šponer JE, Hobza P: Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2′-OH Group of Ribose. J. Chem. Theory Comput., 5(4), 1166-1179, 2009. (DOI)
2008
- Banáš P, Rulíšek L, Hánošová V, Svozil D, Walter NG, Šponer J, Otyepka M: General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility.. J. Phys. Chem. B, 112(35), 11177-11187, 2008. (DOI)
2007
- Meneni SR, Shell SM, Gao L, Jurečka P, Lee W, Šponer J, Zou Y, Chiarelli MP, Cho BP: Spectroscopic and Theoretical Insights into Sequence Effects of Aminofluorene-Induced Conformational Heterogeneity and Nucleotide Excision Repair. Biochemistry, 46(40), 11263-11278, 2007. (DOI)