Vojtech Mlynsky
Vojtech Mlynsky
Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
確認したメール アドレス: ibp.cz - ホームページ
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引用先
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme
V Mlýnský, P Banáš, D Hollas, K Réblová, NG Walter, J Šponer, ...
The journal of physical chemistry B 114 (19), 6642-6652, 2010
852010
Comparison of ab initio, DFT, and semiempirical QM/MM approaches for description of catalytic mechanism of hairpin ribozyme
V Mlýnský, P Banáš, J Sponer, MW van der Kamp, AJ Mulholland, ...
Journal of chemical theory and computation 10 (4), 1608-1622, 2014
492014
Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions (vol 15, pg 3288, 2019)
P Kuhrova, V Mlynsky, M Zgarbova, M Krepl, G Bussi, RB Best, M Otyepka, ...
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 16 (1), 818-819, 2020
47*2020
QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms
V Mlýnský, P Banáš, NG Walter, J Šponer, M Otyepka
The Journal of Physical Chemistry B 115 (47), 13911-13924, 2011
342011
Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations
V Mlýnský, P Kührová, M Zgarbová, P Jurečka, NG Walter, M Otyepka, ...
The Journal of Physical Chemistry B 119 (11), 4220-4229, 2015
222015
The role of an active site Mg 2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations
V Mlýnský, NG Walter, J Šponer, M Otyepka, P Banáš
Physical Chemistry Chemical Physics 17 (1), 670-679, 2015
212015
Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility
V Mlýnský, G Bussi
The journal of physical chemistry letters 9 (2), 313-318, 2018
192018
Exploring RNA structure and dynamics through enhanced sampling simulations
V Mlýnský, G Bussi
https://doi.org/10.1016/j.sbi.2018.01.004, 2017
192017
Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides
V Mlýnský, G Bussi
Rna 23 (5), 712-720, 2017
92017
Fine-tuning of the AMBER RNA force field with a new term adjusting interactions of terminal nucleotides
V Mlynsky, P Kuhrova, T Kuhr, M Otyepka, G Bussi, P Banas, J Sponer
Journal of chemical theory and computation 16 (6), 3936-3946, 2020
72020
Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis
V Mlýnský, P Kührová, P Jurečka, J Sponer, M Otyepka, P Banáš
The Journal of Physical Chemistry B 121 (48), 10828-10840, 2017
42017
Correction to Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions
P Kührová, V Mlýnský, M Zgarbová, M Krepl, G Bussi, RB Best, M Otyepka, ...
Journal of chemical theory and computation 16 (1), 818, 2020
32020
UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations
K Mráziková, V Mlynsky, P Kuhrova, P Pokorná, H Kruse, M Krepl, ...
Journal of Chemical Theory and Computation 16 (12), 7601-7617, 2020
12020
W-RESP: Well-Restrained Electrostatic Potential Derived Charges. Revisiting the Charge Derivation Model.
M Janecek, P Kuhrova, V Mlynsky, M Otyepka, J Sponer, P Banas
bioRxiv, 2020
2020
Tuning the hydrogen-bonding interactions of the AMBER RNA force field
P Kuhrova, V Mlynsky, M Zgarbova, M Krepl, G Bussi, RB Best, M Otyepka, ...
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 37, 50-51, 2019
2019
QM/MM approach to the phosphate cleavage of non-reactive RNA nucleotides
V Mlynsky, G Bussi
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 251, 2016
2016
Structure, Dynamics and Reaction Mechanism of RNA Enzymes
V Mlýnský
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論文 1–17