Miroslav Krepl

发表

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Richard A. Cunha, J. Šponer, Sandro Bottaro, 2018, Chemical reviews.

Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs

J. Šponer, M. Krepl, F. Allain, 2016, Nucleic acids research.

Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration.

J. Šponer, F. Damberger, M. Krepl, 2021, The journal of physical chemistry. B.

Recognition of N6-methyladenosine by the YTHDC1 YTH domain studied by molecular dynamics and NMR spectroscopy: The role of hydration

J. Šponer, F. Damberger, M. Krepl, 2021, bioRxiv.

Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition

J. Šponer, F. Damberger, M. Krepl, 2017, Nucleic acids research.

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.

J. Šponer, G. Bussi, R. Best, 2019, Journal of chemical theory and computation.

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.

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

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

Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations

J. Šponer, G. Bussi, N. Stephanopoulos, 2023, Journal of chemical information and modeling.

Extended molecular dynamics of a c-kit promoter quadruplex

Stephen Neidle, Jaroslav Koca, Shozeb Haider, 2015, Nucleic acids research.

Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing

M. Okoniewski, M. Zavolan, J. Šponer, 2021, Nature communications.

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

J. Šponer, T. Cheatham, J. Koča, 2012, Journal of chemical theory and computation.

Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase

J. Šponer, M. Krepl, J. Poznański, 2017, Nucleic acids research.

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

Hao Yan, J. Šponer, N. Stephanopoulos, 2022, Nature Communications.

RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution

J. Šponer, M. Krepl, J. Poznański, 2019, Nature Communications.

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.

MD simulations reveal the basis for dynamic assembly of Hfq–RNA complexes

J. Šponer, B. Luisi, M. Krepl, 2021, The Journal of biological chemistry.

Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study

Gabriele Varani, Paolo Carloni, Fan Yang, 2018, PLoS Comput. Biol..

QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods.

J. Šponer, M. Krepl, H. Kruse, 2018, Journal of chemical theory and computation.

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations

J. Šponer, M. Krepl, V. Mlýnský, 2023, bioRxiv.

Residues flanking the ARKme3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations.

J. Šponer, M. Krepl, Pavlína Pokorná, 2020, Biochimica et biophysica acta. General subjects.

Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network.

J. Šponer, E. Bártová, M. Krepl, 2019, Journal of chemical theory and computation.

Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops.

K. Réblová, J. Šponer, J. Koča, 2013, The journal of physical chemistry. B.

MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, l-Histidine Ligand, and Mg2.

J. Šponer, M. Krepl, H. Kruse, 2017, Journal of chemical theory and computation.

Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM

J. Šponer, J. Boudet, M. Krepl, 2019, Proceedings of the National Academy of Sciences.

Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field

J. Šponer, M. Krepl, V. Mlýnský, 2022, bioRxiv.

UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations.

J. Šponer, M. Otyepka, P. Banáš, 2020, Journal of chemical theory and computation.

UNCG RNA tetraloop as a formidable force-field challenge for MD simulations

J. Šponer, M. Otyepka, P. Banáš, 2020, bioRxiv.

Improving the Performance of the RNA Amber Force Field by Tuning the Hydrogen-Bonding Interactions

J. Šponer, G. Bussi, R. Best, 2018, bioRxiv.

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.

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

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

Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory.

J. Šponer, M. Otyepka, P. Banáš, 2013, Physical chemistry chemical physics : PCCP.

Combining NMR Spectroscopy and Molecular Dynamic Simulations to Solve and Analyze the Structure of Protein-RNA Complexes.

J. Šponer, M. Krepl, S. Campagne, 2019, Methods in enzymology.

Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations

J. Šponer, M. Krepl, S. Campagne, 2022, bioRxiv.

Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: molecular dynamics thermodynamics integration study.

J. Šponer, M. Otyepka, P. Banáš, 2013, The journal of physical chemistry. B.

Phosphorothioate substitutions in RNA structure studied by molecular dynamics simulations, QM/MM calculations and NMR experiments

J. Šponer, J. Wöhnert, M. Krepl, 2020, bioRxiv.

Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination

J. Šponer, Olivier Duss, F. Damberger, 2017, Nature Communications.

Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations

J. Šponer, M. Otyepka, P. Banáš, 2023, bioRxiv.

J. Šponer, M. Otyepka, P. Banáš, 2015, The journal of physical chemistry. B.

Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase

J. Šponer, T. Ha, M. Krepl, 2017, The Journal of Biological Chemistry.

Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations

V. Mlýnský, Miroslav Krepl, Petr Stadlbauer, 2024, bioRxiv.

Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field

J. Šponer, G. Bussi, P. Banáš, 2022, Journal of chemical theory and computation.

Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions".

J. Šponer, G. Bussi, R. Best, 2019, Journal of chemical theory and computation.

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

Jaroslav Koča, Thomas E. Cheatham, Jiří Šponer, 2013, Nucleic acids research.

DNA Damage Changes Distribution Pattern and Levels of HP1 Protein Isoforms in the Nucleolus and Increases Phosphorylation of HP1β-Ser88

J. Šponer, S. Legartová, S. Kozubek, 2019, Cells.

Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops.

K. Réblová, J. Šponer, J. Koča, 2013, The journal of physical chemistry. B.

Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease.

Jaroslav Koča, Michal Otyepka, Carolina Estarellas, 2015, Biochimica et biophysica acta.