M. Havrila

发表

Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective.

J. Šponer, H. Kruse, Rafał Szabla, 2016, The journal of physical chemistry. B.

QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches.

J. Šponer, H. Kruse, M. Havrila, 2014, Journal of chemical theory and computation.

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

J. Šponer, R. Stefl, M. Otyepka, 2015, Journal of chemical theory and computation.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

Michal Otyepka, Marek Havrila, Petr Jurečka, 2014, The journal of physical chemistry letters.

Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations.

J. Šponer, M. Krepl, S. Haider, 2018, Journal of chemical theory and computation.

Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

J. Šponer, M. Otyepka, J. Mergny, 2018, Nucleic acids research.

Role of S-turn2 in the structure, dynamics, and function of mitochondrial ribosomal A-site. A bioinformatics and molecular dynamics simulation study.

K. Réblová, J. Šponer, J. Trylska, 2014, The journal of physical chemistry. B.

Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field.

J. Šponer, M. Otyepka, P. Banáš, 2017, The journal of physical chemistry. B.

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.

Michal Otyepka, Marek Havrila, Petr Jurečka, 2015, The journal of physical chemistry. B.

Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.

Craig L. Zirbel, K. Réblová, J. Šponer, 2013, The journal of physical chemistry. B.

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes.

Michal Otyepka, Marek Havrila, Jiří Šponer, 2017, Journal of chemical theory and computation.

How to understand atomistic molecular dynamics simulations of RNA and protein–RNA complexes?

Michal Otyepka, Marek Havrila, Petr Jurečka, 2017, Wiley interdisciplinary reviews. RNA.