| 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 | 123* | 2020 |
| 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 | 97 | 2010 |
| 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 | 72 | 2014 |
| 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 | 47 | 2020 |
| 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 | 42 | 2015 |
| Exploring RNA structure and dynamics through enhanced sampling simulations V Mlýnský, G Bussi https://doi.org/10.1016/j.sbi.2018.01.004, 2017 | 40 | 2017 |
| 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 | 39 | 2020 |
| QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms V Mlynsky, P Banáš, NG Walter, J Sponer, M Otyepka The Journal of Physical Chemistry B 115 (47), 13911-13924, 2011 | 39 | 2011 |
| 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 | 36 | 2022 |
| 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 | 36 | 2018 |
| 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 | 28 | 2015 |
| Automatic learning of hydrogen-bond fixes in the AMBER RNA force field T Frohlking, V Mlýnský, M Janeček, P Kührová, M Krepl, P Banáš, ... Journal of Chemical Theory and Computation 18 (7), 4490-4502, 2022 | 27 | 2022 |
| 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 | 25 | 2021 |
| Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field M Krepl, P Pokorná, V Mlýnský, P Stadlbauer, J Šponer Nucleic Acids Research 50 (21), 12480-12496, 2022 | 20 | 2022 |
| Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes P Kührová, V Mlýnský, M Otyepka, J Šponer, P Banáš Journal of Chemical Information and Modeling 63 (7), 2133-2146, 2023 | 14 | 2023 |
| Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations V Mlynsky, P Kuhrova, P Stadlbauer, M Krepl, M Otyepka, P Banas, ... Journal of Chemical Theory and Computation 19 (22), 8423-8433, 2023 | 13 | 2023 |
| Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides V Mlýnský, G Bussi Rna 23 (5), 712-720, 2017 | 13 | 2017 |
| Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations Z Zhang, J Sponer, G Bussi, V Mlynsky, P Sulc, CR Simmons, ... Journal of Chemical Information and Modeling 63 (9), 2794-2809, 2023 | 8 | 2023 |
| 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 | 6 | 2021 |
| 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 | 5 | 2017 |
Pavel BanášCzech Advanced Technology and Research Institute CATRIN, Palacky University OlomoucVerified email at upol.cz