Miroslav Krepl

Scopus Author ID ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 35

Top Venues

Journal of chemical information and modeling

Journal of chemical theory and computation

Nucleic acids research

The journal of physical chemistry. B

Palacký University, Olomouc

Masaryk University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Palacký University, Olomouc Jan 01 2017

Czechia

Researcher :: Department of Physical Chemistry

Institute of Biophysics of the CAS, v. v. i. Jul 01 2010

Czechia

Researcher :: Department of Structure and Dynamics of Nucleic Acids

Education History

Masaryk University Sep 01 2008 - Dec 12 2017

Czechia

PHD

Publications

Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling 64 (9) (2024)
Barbora Knappeová, Vojtěch Mlýnský, Martin Pykal, Jiřı Šponer, Pavel Banáš, Michal Otyepka, Miroslav Krepl
Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes. Journal of chemical theory and computation 20 (15) (2024)
Jennifer Vögele, Elke Duchardt-Ferner, Jasleen Kaur Bains, Bozana Knezic, Anna Wacker, Christian Sich, Julia E Weigand, Jiří Šponer, Harald Schwalbe, Miroslav Krepl, Jens Wöhnert
Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA. Nucleic acids research 52 (11) (2024)
Jennifer Vögele, Elke Duchardt-Ferner, Jasleen Kaur Bains, Bozana Knezic, Anna Wacker, Christian Sich, Julia E Weigand, Jiří Šponer, Harald Schwalbe, Miroslav Krepl, Jens Wöhnert
Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA. Nucleic acids research (2024)
Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling (2024)
Jennifer Vögele, Elke Duchardt-Ferner, Jasleen Kaur Bains, Bozana Knezic, Anna Wacker, Christian Sich, Julia E Weigand, Jiří Šponer, Harald Schwalbe, Miroslav Krepl, Jens Wöhnert
Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA. Nucleic acids research 52 (11) (2024)
Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling 64 (9) (2024)
Barbora Knappeová, Vojtěch Mlýnský, Martin Pykal, Jiřı Šponer, Pavel Banáš, Michal Otyepka, Miroslav Krepl
Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes. Journal of chemical theory and computation 20 (15) (2024)
Barbora Knappeová, Vojtěch Mlýnský, Martin Pykal, Jiřı Šponer, Pavel Banáš, Michal Otyepka, Miroslav Krepl
Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes. Journal of chemical theory and computation (2024)
Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling 64 (9) (2024)
Jennifer Vögele, Elke Duchardt-Ferner, Jasleen Kaur Bains, Bozana Knezic, Anna Wacker, Christian Sich, Julia E Weigand, Jiří Šponer, Harald Schwalbe, Miroslav Krepl, Jens Wöhnert
Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA. Nucleic acids research (2024)
Barbora Knappeová, Vojtěch Mlýnský, Martin Pykal, Jiřı Šponer, Pavel Banáš, Michal Otyepka, Miroslav Krepl
Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes. Journal of chemical theory and computation 20 (15) (2024)
Fred F Damberger, Miroslav Krepl, Rajika Arora, Irene Beusch, Christophe Maris, Georg Dorn, Jiří Šponer, Sapna Ravindranathan, Frédéric Hai-Trieu Allain
N-terminal domain of polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition. Nucleic acids research (2024)
Jennifer Vögele, Elke Duchardt-Ferner, Jasleen Kaur Bains, Bozana Knezic, Anna Wacker, Christian Sich, Julia E Weigand, Jiří Šponer, Harald Schwalbe, Miroslav Krepl, Jens Wöhnert
Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA. Nucleic acids research 52 (11) (2024)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling (2023)
Petr Stadlbauer, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. Journal of chemical information and modeling (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Vojtěch Mlýnský, Petra Kührová, Petr Stadlbauer, Miroslav Krepl, Michal Otyepka, Pavel Banáš, Jiřı Šponer
Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations. Journal of chemical theory and computation (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Miroslav Krepl, Pavlína Pokorná, Vojtěch Mlýnský, Petr Stadlbauer, Jiří Šponer
Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field. Nucleic acids research (2022)
Thorben Fröhlking, Vojtěch Mlýnský, Michal Janeček, Petra Kührová, Miroslav Krepl, Pavel Banáš, Jiřı Šponer, Giovanni Bussi
Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field. Journal of chemical theory and computation 18 (7) (2022)
Pavlína Pokorná, Miroslav Krepl, Sébastien Campagne, Jiřı Šponer
Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations. The journal of physical chemistry. B 126 (45) (2022)
Chad R Simmons, Tara MacCulloch, Miroslav Krepl, Michael Matthies, Alex Buchberger, Ilyssa Crawford, Jiřı Šponer, Petr Sulc, Nicholas Stephanopoulos, Hao Yan
The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly. Nature communications 13 (1) (2022)
Zhengyue Zhang, Jennifer Vögele, Klaudia Mráziková, Holger Kruse, Xiaohui Cang, Jens Wöhnert, Miroslav Krepl, Jiřı Šponer
Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments. The journal of physical chemistry. B 125 (3) (2021)
Miroslav Krepl, Fred Franz Damberger, Christine von Schroetter, Dominik Theler, Pavlína Pokorná, Frédéric H-T Allain, Jiřı Šponer
Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration. The journal of physical chemistry. B 125 (28) (2021)
Antoine Cléry, Miroslav Krepl, Cristina K X Nguyen, Ahmed Moursy, Hadi Jorjani, Maria Katsantoni, Michal Okoniewski, Nitish Mittal, Mihaela Zavolan, Jiřı Šponer, Frédéric Hai-Trieu Allain
Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing. Nature communications 12 (1) (2021)
Klaudia Mráziková, Vojtěch Mlýnský, Petra Kührová, Pavlína Pokorná, Holger Kruse, Miroslav Krepl, Michal Otyepka, Pavel Banáš, Jiřı Šponer
UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations. Journal of chemical theory and computation 16 (12) (2020)
Pavlína Pokorná, Miroslav Krepl, Eva Bártová, Jiřı Šponer
Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network. Journal of chemical theory and computation 15 (10) (2019)
Petra Kührová, Vojtěch Mlýnský, Marie Zgarbová, Miroslav Krepl, Giovanni Bussi, Robert B Best, Michal Otyepka, Jiřı Šponer, Pavel Banáš
Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions". Journal of chemical theory and computation 16 (1) (2019)
Karolina Maria Górecka, Miroslav Krepl, Aleksandra Szlachcic, Jarosław T Poznański, Jiřı Šponer, Marcin Nowotny
RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution. Nature communications 10 (1) (2019)
Nina Ripin, Julien Boudet, Malgorzata M Duszczyk, Alexandra Hinniger, Michael Faller, Miroslav Krepl, Abhilash Gadi, Robert J Schneider, Jiří Šponer, Nicole C Meisner-Kober, Frédéric H-T Allain
Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM. Proceedings of the National Academy of Sciences of the United States of America 116 (8) (2019)
Petra Kührová, Vojtěch Mlýnský, Marie Zgarbová, Miroslav Krepl, Giovanni Bussi, Robert B Best, Michal Otyepka, Jiřı Šponer, Pavel Banáš
Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. Journal of chemical theory and computation 15 (5) (2019)
Anna Bochicchio, Miroslav Krepl, Fan Yang, Gabriele Varani, Jiřı Šponer, Paolo Carloni
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study. PLoS computational biology 14 (12) (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Miroslav Krepl