| 1 |
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Sponer J, Bussi G, Krepl M, Banas P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jureacka P, Walter NG, Otyepka M
Chemical Reviews, 118(8), 4177, 2018 |
| 2 |
Noncanonical alpha/gamma Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field
Zgarbova M, Jurecka P, Banas P, Havrila M, Sponer J, Otyepka M
Journal of Physical Chemistry B, 121(11), 2420, 2017 |
| 3 |
Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis
Mlynsky V, Kuhrova P, Jurecka P, Sponer J, Otyepka M, Banas P
Journal of Physical Chemistry B, 121(48), 10828, 2017 |
| 4 |
Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields
Havrila M, Zgarbova M, Jurecka P, Banas P, Krepl M, Otyepka M, Sponer J
Journal of Physical Chemistry B, 119(49), 15176, 2015 |
| 5 |
Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations
Mlynsky V, Kuhrova P, Zgarbova M, Jurecka P, Walter NG, Otyepka M, Sponer J, Banas P
Journal of Physical Chemistry B, 119(11), 4220, 2015 |
| 6 |
Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study
Krepl M, Otyepka M, Banas P, Sponer J
Journal of Physical Chemistry B, 117(6), 1872, 2013 |
| 7 |
Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration
Besseova I, Banas P, Kuhrova P, Kosinova P, Otyepka M, Sponer J
Journal of Physical Chemistry B, 116(33), 9899, 2012 |
| 8 |
Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study
Banas P, Sklenovsky P, Wedekind JE, Sponer J, Otyepka M
Journal of Physical Chemistry B, 116(42), 12721, 2012 |
| 9 |
Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base-Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations
Zgarbova M, Jurecka P, Banas P, Otyepka M, Sponer JE, Leontis NB, Zirbel CL, Sponer J
Journal of Physical Chemistry A, 115(41), 11277, 2011 |
| 10 |
QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms
Mlynsky V, Banas P, Walter NG, Sponer J, Otyepka M
Journal of Physical Chemistry B, 115(47), 13911, 2011 |
