P. Stadlbauer

发表

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

J. Šponer, R. Stefl, M. Otyepka, 2015, Journal of chemical theory and computation.

Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.

D. Wales, J. Šponer, P. Derreumaux, 2016, Journal of chemical theory and computation.

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

J. Šponer, T. Cheatham, J. Koča, 2012, Journal of chemical theory and computation.

Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies.

J. Šponer, G. Bussi, M. Otyepka, 2016, Biochimica et biophysica acta. General subjects.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

Michal Otyepka, Marek Havrila, Petr Jurečka, 2014, The journal of physical chemistry letters.

Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations.

J. Šponer, M. Krepl, S. Haider, 2018, Journal of chemical theory and computation.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

J. Šponer, G. Bussi, M. Otyepka, 2017, Journal of chemical theory and computation.

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

J. Šponer, J. Koča, G. Bussi, 2015, Nucleic acids research.

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations.

J. Šponer, T. Cheatham, J. Koča, 2014, Biochimie.

Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes

J. Šponer, M. Otyepka, P. Banáš, 2019, Nucleic acids research.

Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

J. Šponer, M. Otyepka, J. Mergny, 2018, Nucleic acids research.

Insights into G-Quadruplex-Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding.

J. Šponer, M. Otyepka, J. Mergny, 2021, Journal of chemical theory and computation.

Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field

J. Šponer, M. Krepl, V. Mlýnský, 2022, bioRxiv.

Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label.

J. Šponer, Xiaojun Zhang, Yuan Ding, 2016, Biochemistry.

G-Quadruplex formation by DNA sequences deficient in guanines: Two tetrad parallel quadruplexes do not fold intramolecularly.

J. Šponer, J. Mergny, Jan Palacký, 2021, Chemistry.

2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions

J. Šponer, J. Rak, H. Kruse, 2021, Nature Communications.

Insight into formation propensity of pseudocircular DNA G-hairpins

J. Šponer, J. Plavec, P. Stadlbauer, 2021, Nucleic acids research.

Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding

J. Šponer, M. Otyepka, J. Mergny, 2020, bioRxiv.

Stability of Two-quartet G-quadruplexes and Their Dimers in Atomistic Simulations.

J. Šponer, M. Otyepka, J. Mergny, 2020, Journal of chemical theory and computation.

Molecular dynamics simulations of G-quadruplexes: The basic principles and their application to folding and ligand binding

Jiri Sponer, Barira Islam, Petr Stadlbauer, 2020 .

Stability of Two-quartet G-quadruplexes and Their Dimers in Atomistic Simulations

J. Šponer, M. Otyepka, J. Mergny, 2019, bioRxiv.

Sequential electron transfer governs the UV-induced self-repair of DNA photolesions

J. Šponer, H. Kruse, Rafał Szabla, 2018, Chemical science.

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes.

Michal Otyepka, Marek Havrila, Jiří Šponer, 2017, Journal of chemical theory and computation.

Can we Execute Reliable MM-PBSA Free Energy Computations of Relative Energies of Different Guanine Quadruplex Folds ?

J. Šponer, S. Neidle, S. Haider, 2017 .

Can We Execute Reliable MM-PBSA Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds?

Stephen Neidle, Shozeb Haider, Barira Islam, 2016, The journal of physical chemistry. B.

Extended molecular dynamics of a c-kit promoter quadruplex

Stephen Neidle, Jaroslav Koca, Shozeb Haider, 2015, Nucleic acids research.

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

Jaroslav Koča, Thomas E. Cheatham, Jiří Šponer, 2013, Nucleic acids research.

Primitive RNA-catalysis with guanine-rich oligonucleotide sequences – the case of a (GGC)3 nonamer

J. Šponer, J. Šponer, G. Costanzo, 2020, bioRxiv.

Tetraloop-like geometries could form the basis of the catalytic activity of the most ancient ribooligonucleotides.

J. Šponer, J. Šponer, G. Costanzo, 2015, Chemistry.

Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine

J. Šponer, R. Improta, P. Banáš, 2021, International Journal of Biological Macromolecules.

Exploring Sequence Space to Design Controllable G-quadruplex Topology Switches

J. Šponer, H. Ju, J. Mergny, 2021, CCS Chemistry.

The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology

J. Šponer, G. Salgado, H. Ju, 2021, Nucleic acids research.

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations

J. Šponer, M. Krepl, V. Mlýnský, 2023, bioRxiv.