List of works - Miroslav Krepl

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

scientific article published on 21 September 2017

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

scientific article published on 14 June 2022

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

article by Arnošt Mládek et al published 2013 in Physical Chemistry Chemical Physics

Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops

article

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

scientific article published on 3 February 2015

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

scientific article

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

scientific article published on 19 December 2019

Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study

article

Extended molecular dynamics of a c-kit promoter quadruplex

scientific article

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

scientific article published on 10 November 2016

IMPROVING THE PERFORMANCE OF THE RNA AMBER FORCE FIELD BY TUNING THE HYDROGEN-BONDING INTERACTIONS

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

scientific article published on 02 April 2019

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

scientific article published on 16 October 2017

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

scientific article published on 9 November 2017

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

scientific article

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

article

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

scientific article published on 04 February 2019

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

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

scientific article published on 24 October 2014

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

scientific article published on 3 January 2018

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

scientific article

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

scientific article published on 18 September 2019

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

scientific article published on 10 September 2019

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

scientific article published on 21 May 2013

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

scientific article

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

scientific article published on 18 May 2016

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

scientific article published on 20 November 2020

List of works by Miroslav Krepl

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

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

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

Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops

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

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

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

Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study

Extended molecular dynamics of a c-kit promoter quadruplex

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

IMPROVING THE PERFORMANCE OF THE RNA AMBER FORCE FIELD BY TUNING THE HYDROGEN-BONDING INTERACTIONS

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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