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Petr Stadlbauer · SciRah

Researcher profile · Semantic Scholar

Petr Stadlbauer

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Petr Stadlbauer — researcher profile on SciRah

h-index: 23
Works: 54
Citations: 1,595

Most-cited papers

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA
Miroslav Krepl, Marie Zgarbová, Petr Stadlbauer, M. Otyepka +5 more
2012Journal of Chemical Theory and Computation236 citations Open access
Semantic Scholar
Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.
J. Šponer, P. Banáš, P. Jurečka, Marie Zgarbová +5 more
2014Journal of Physical Chemistry Letters161 citations Open access
Semantic Scholar
Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies.
J. Šponer, G. Bussi, Petr Stadlbauer, Petra Kührová +5 more
2016Biochimica et Biophysica Acta - General Subjects103 citations Open access
Semantic Scholar
Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations
Petr Stadlbauer, Miroslav Krepl, T. Cheatham, J. Koča +1 more
2013Nucleic Acids Research102 citations Open access
Semantic Scholar
Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?
Miroslav Krepl, Marek Havrila, Petr Stadlbauer, P. Banáš +4 more
2015Journal of Chemical Theory and Computation72 citations
Semantic Scholar
Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations.
Petr Stadlbauer, L. Trantírek, T. Cheatham, J. Koča +1 more
2014Biochimie71 citations Open access
Semantic Scholar
Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations
Petr Stadlbauer, Petra Kührová, P. Banáš, J. Koča +4 more
2015Nucleic Acids Research61 citations Open access
Semantic Scholar
Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes.
Marek Havrila, Petr Stadlbauer, Barira Islam, M. Otyepka +1 more
2017Journal of Chemical Theory and Computation55 citations
Semantic Scholar
Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes
Petr Stadlbauer, Petra Kührová, Lukáš Vicherek, P. Banáš +3 more
2019Nucleic Acids Research53 citations Open access
Semantic Scholar
The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology
Jie-Lin Chen, Mingpan Cheng, G. Salgado, Petr Stadlbauer +8 more
2021Nucleic Acids Research51 citations Open access
Semantic Scholar
Extended molecular dynamics of a c-kit promoter quadruplex
Barira Islam, Petr Stadlbauer, Miroslav Krepl, J. Koča +3 more
2015Nucleic Acids Research51 citations Open access
Semantic Scholar
Structure of a Stable G-Hairpin.
Martin Gajarský, M. Živkovič, Petr Stadlbauer, B. Pagano +6 more
2017Journal of the American Chemical Society49 citations
Semantic Scholar
Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.
Petr Stadlbauer, L. Mazzanti, T. Cragnolini, D. Wales +3 more
2016Journal of Chemical Theory and Computation45 citations Open access
Semantic Scholar
Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations
Barira Islam, Petr Stadlbauer, Alejandro Gil-Ley, G. Pérez-Hernández +6 more
2017Journal of Chemical Theory and Computation41 citations Open access
Semantic Scholar
Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems
V. Mlýnský, Petra Kührová, M. Pykal, Miroslav Krepl +4 more
2024bioRxiv34 citations Open access
Semantic Scholar
Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding
Petr Stadlbauer, Barira Islam, M. Otyepka, Jie-Lin Chen +4 more
2020bioRxiv32 citations Open access
Semantic Scholar
Structural dynamics of propeller loop: towards folding of RNA G-quadruplex
Marek Havrila, Petr Stadlbauer, Petra Kührová, P. Banáš +3 more
2018Nucleic Acids Research31 citations Open access
Semantic Scholar
Can We Execute Reliable MM-PBSA Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds?
Barira Islam, Petr Stadlbauer, S. Neidle, S. Haider +1 more
2016Journal of Physical Chemistry B30 citations Open access
Semantic Scholar
Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations.
Barira Islam, Petr Stadlbauer, Miroslav Krepl, Marek Havrila +2 more
2018Journal of Chemical Theory and Computation29 citations
Semantic Scholar
Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations
V. Mlýnský, Petra Kührová, Petr Stadlbauer, Miroslav Krepl +3 more
2023bioRxiv26 citations Open access
Semantic Scholar
2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions
Rafał Szabla, Magdalena Zdrowowicz, Paulina Spisz, Nicholas J. Green +4 more
2021Nature Communications25 citations Open access
Semantic Scholar
Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field
Miroslav Krepl, P. Pokorná, V. Mlýnský, Petr Stadlbauer +1 more
2022bioRxiv24 citations Open access
Semantic Scholar
Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label
Xiao-Jun Zhang, Cui-Xia Xu, R. Di Felice, J. Šponer +6 more
2015Biochemistry23 citations Open access
Semantic Scholar
Stability of Two-quartet G-quadruplexes and Their Dimers in Atomistic Simulations
Barira Islam, Petr Stadlbauer, M. Vorlíčková, J. Mergny +2 more
2019bioRxiv21 citations Open access
Semantic Scholar
G-Quadruplex formation by DNA sequences deficient in guanines: Two tetrad parallel quadruplexes do not fold intramolecularly.
I. Kejnovská, Petr Stadlbauer, L. Trantírek, D. Renčiuk +7 more
2021Chemistry20 citations
Semantic Scholar
Exploring Sequence Space to Design Controllable G-quadruplex Topology Switches
Jie-Lin Chen, Mingpan Cheng, Petr Stadlbauer, J. Šponer +3 more
2021CCS Chemistry19 citations Open access
Semantic Scholar
Sequential electron transfer governs the UV-induced self-repair of DNA photolesions
Rafał Szabla, H. Kruse, Petr Stadlbauer, J. Šponer +1 more
2018Chemical Science19 citations Open access
Semantic Scholar
Molecular dynamics simulations reveal the parallel stranded d(GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble.
P. Pokorná, V. Mlýnský, G. Bussi, J. Šponer +1 more
2024International Journal of Biological Macromolecules14 citations Open access
Semantic Scholar
Tetraloop-like geometries could form the basis of the catalytic activity of the most ancient ribooligonucleotides.
Petr Stadlbauer, J. Sponer, G. Costanzo, E. di Mauro +2 more
2015Chemistry10 citations
Semantic Scholar
Atomistic Insights Into Interaction of Doxorubicin With DNA: From Duplex to Nucleosome
Andrea Nedelníková, Petr Stadlbauer, Michal Otyepka, Petra Kührová +1 more
2025Journal of Computational Chemistry8 citations Open access
Semantic Scholar
Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern
C. L. Kufner, Sarah J Crucilla, Dian Ding, Petr Stadlbauer +4 more
2023Chemical Science8 citations Open access
Semantic Scholar
Topology of DNA G-Quadruplexes Can Be Harnessed in Holliday Junction-Based DNA Suprastructures to Control and Optimize Their Biocatalytic Properties
De-Hui Qiu, Mingpan Cheng, Petr Stadlbauer, Jie-Lin Chen +8 more
2023ACS Catalysis8 citations
Semantic Scholar
DNA Quadruplex Structure with a Unique Cation Dependency.
Martin Gajarský, Petr Stadlbauer, J. Šponer, Anne Cucchiarini +5 more
2023Angewandte Chemie8 citations Open access
Semantic Scholar
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations
Petr Stadlbauer, V. Mlýnský, Miroslav Krepl, J. Šponer
2023bioRxiv8 citations Open access
Semantic Scholar
Molecular dynamics simulations of G-quadruplexes: The basic principles and their application to folding and ligand binding
J. Šponer, Barira Islam, Petr Stadlbauer, S. Haider
20208 citations
Semantic Scholar
Insight into formation propensity of pseudocircular DNA G-hairpins
M. Živkovič, Martin Gajarský, Kateřina Beková, Petr Stadlbauer +7 more
2021Nucleic Acids Research7 citations Open access
Semantic Scholar
Structural basis of bis-quinolinium ligands binding to quadruplex–duplex hybrids from PIM1 oncogene
Anirban Ghosh, J. Harnoš, Petr Stadlbauer, J. Sponer +2 more
2025Nucleic Acids Research6 citations Open access
Semantic Scholar
Computer Folding of Parallel DNA G‐Quadruplex: Hitchhiker's Guide to the Conformational Space
Michael Janeček, Petra Kührová, V. Mlýnský, Petr Stadlbauer +4 more
2024Journal of Computational Chemistry6 citations Open access
Semantic Scholar
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations
Zhengyue Zhang, V. Mlýnský, Miroslav Krepl, J. Šponer +1 more
2024bioRxiv5 citations Open access
Semantic Scholar
UV-induced hydrogen transfer in DNA base pairs promoted by dark nπ* states.
Kinga E. Szkaradek, Petr Stadlbauer, J. Šponer, R. Góra +1 more
2019Chemical Communications5 citations Open access
Semantic Scholar
Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge
Andrea Nedelníková, Petr Stadlbauer, P. Banáš, J. Šponer +3 more
2025Journal of Chemical Information and Modeling4 citations
Semantic Scholar
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways
P. Pokorná, V. Mlýnský, J. Šponer, Petr Stadlbauer
2025Nucleic Acids Research3 citations Open access
Semantic Scholar
Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine.
H. Asha, Petr Stadlbauer, Lara Martínez-Fernández, P. Banáš +3 more
2021International Journal of Biological Macromolecules3 citations Open access
Semantic Scholar
Correction to "Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes".
Marek Havrila, Petr Stadlbauer, Barira Islam, M. Otyepka +1 more
2018Journal of Chemical Theory and Computation3 citations Open access
Semantic Scholar
RNA G-Quadruplex Emerges from a Coil-Like Ensemble via Multiple Pathways
P. Pokorná, V. Mlýnský, J. Šponer, Petr Stadlbauer
2025bioRxiv1 citations Open access
Semantic Scholar
Parallel G-quadruplex folds via multiple paths involving G-tract stacking and structuring from coil ensemble
P. Pokorná, V. Mlýnský, G. Bussi, J. Šponer +1 more
2023bioRxiv1 citations Open access
Semantic Scholar
DNA guanine quadruplexes: When less is more.
H. Kašparová, Petr Stadlbauer, Martin Gajarský, Tereza Mikešová +3 more
2026International Journal of Biological Macromolecules0 citations Open access
Semantic Scholar
Parallel DNA Holliday Junctions: Myth or Reality? An Atomistic Molecular Dynamics Study
Toon Lemmens, J. Šponer, Petr Stadlbauer, Miroslav Krepl
2026bioRxiv0 citations Open access
Semantic Scholar
Primitive RNA-catalysis with guanine-rich oligonucleotide sequences – the case of a (GGC)3 nonamer
G. Costanzo, A. Cirigliano, S. Pino, A. Giorgi +6 more
2020bioRxiv0 citations Open access
Semantic Scholar
Electronic Supplementary Information (ESI) for: UV-induced hydro- gen transfer in DNA base pairs promoted by dark nπ∗ states†
Kinga E. Szkaradek, Petr Stadlbauer, J. Sponer, R. Góra +1 more
20190 citations
Semantic Scholar

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