Výpis publikací

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://doi.org/10.1093/nar/gkac1106.

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://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://doi.org/10.1016/j.bbagen.2016.12.008.

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://doi.org/10.1021/jacs.6b10786.

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://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://doi.org/10.1021/acs.jctc.6b00667.

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://doi.org/10.1021/acs.biochem.5b01189.

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://doi.org/10.1021/ct5008108.

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://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://doi.org/10.1093/nar/gkv994.

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.

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.

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://doi.org/10.1002/chem.201406140.

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://doi.org/10.1021/jz500557y.

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://doi.org/10.1016/j.biochi.2014.07.009.

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://doi.org/10.1093/nar/gkt412.

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://doi.org/10.1021/ct300275s.