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Vojtech Mlynsky
Vojtech Mlynsky
Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
Email verificata su ibp.cz - Home page
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Citata da
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Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H+ Forms Are Most Consistent with Crystal Structures of Hairpin …
V Mlynsky, P Banáš, D Hollas, K Réblová, NG Walter, J Sponer, ...
The journal of physical chemistry B 114 (19), 6642-6652, 2010
902010
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
66*2020
Comparison of ab initio, DFT, and semiempirical QM/MM approaches for description of catalytic mechanism of hairpin ribozyme
V Mlynsky, P Banas, J Sponer, MW van der Kamp, AJ Mulholland, ...
Journal of chemical theory and computation 10 (4), 1608-1622, 2014
532014
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
302015
Exploring RNA structure and dynamics through enhanced sampling simulations
V Mlýnský, G Bussi
https://doi.org/10.1016/j.sbi.2018.01.004, 2017
272017
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
262018
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
232015
Fine-tuning of the AMBER RNA force field with a new term adjusting interactions of terminal nucleotides
V Mlýnský, P Kührová, T Kühr, M Otyepka, G Bussi, P Banáš, ...
Journal of chemical theory and computation 16 (6), 3936-3946, 2020
222020
Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides
V Mlýnský, G Bussi
Rna 23 (5), 712-720, 2017
122017
UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations
K Mráziková, V Mlýnský, P Kührová, P Pokorná, H Kruse, M Krepl, ...
Journal of chemical theory and computation 16 (12), 7601-7617, 2020
112020
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
Journal of Chemical Theory and Computation 17 (6), 3495-3509, 2021
72021
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
Automatic learning of hydrogen-bond fixes in an AMBER RNA force field
T Fröhlking, V Mlýnský, M Janeček, P Kührová, M Krepl, P Banáš, ...
arXiv preprint arXiv:2201.04078, 2022
32022
Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy) Ribose··· Nucleobase Lone-Pair··· π Contacts in Nucleic Acids
K Mráziková, J Sponer, V Mlýnský, P Auffinger, H Kruse
Journal of Chemical Information and Modeling 61 (11), 5644-5657, 2021
22021
Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications
V Mlýnský, M Janeček, P Kührová, T Fröhlking, M Otyepka, G Bussi, ...
Journal of Chemical Theory and Computation 18 (4), 2642-2656, 2022
12022
Multiscale modelling of phosphate… π contacts in RNA U-turns reveals AMBER force-field deficiencies
K Mráziková, H Kruse, V Mlýnský, P Auffinger, J Šponer
2022
Spontaneous binding of single-stranded RNAs to RRM proteins visualised by unbiased atomistic simulations with rescaled RNA force field
M Krepl, P Pokorna, V Mlynsky, P Stadlbauer, J Sponer
bioRxiv, 2022
2022
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
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
Il sistema al momento non puň eseguire l'operazione. Riprova piů tardi.
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