| 1 |
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 |
| 2 |
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 |
| 3 |
Noncovalent Interactions by Quantum Monte Carlo
Dubecky M, Mitas L, Jurecka P
Chemical Reviews, 116(9), 5188, 2016 |
| 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 |
Coarse-Grain Simulations of Skin Ceramide NS with Newly Derived Parameters Clarify Structure of Melted Phase
Sovova Z, Berka K, Otyepka M, Jurecka P
Journal of Physical Chemistry B, 119(10), 3988, 2015 |
| 6 |
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 |
| 7 |
Adsorption of Small Organic Molecules on Graphene
Lazar P, Karlicky F, Jurecka P, Kocman M, Otyepkova E, Safarova K, Otyepka M
Journal of the American Chemical Society, 135(16), 6372, 2013 |
| 8 |
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 |
| 9 |
Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories
Riley KE, Pitonak M, Jurecka P, Hobza P
Chemical Reviews, 110(9), 5023, 2010 |
| 10 |
Resolution of identity density functional theory augmented with an empirical dispersion term (RI-DFT-D): A promising tool for studying isolated small peptides
Cerny J, Jurecka P, Hobza P, Valdes H
Journal of Physical Chemistry A, 111(6), 1146, 2007 |
