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Palacký University, Olomouc: Olomouc, CZ

2006-06-01 to present | Associate Proffessor (Department of Physical Chemistry)
Employment
Source: Self-asserted source
Petr Jurecka

Works (50 of 79)

Items per page:
Page 1 of 2

Continuous B-to A-Transition in Protein-DNA Binding-How Well Is It Described by Current AMBER Force Fields?

bioRxiv
2022 | Journal article
Contributors: Jurečka, Petr; Zgarbová, Marie; Čerǹy, Filip; Salomon, Jan
Source: Self-asserted source
Petr Jurecka

Probabilistic Interpretation of NMR J-Couplings Determines BI--BII State Equilibria in DNA

Journal of Chemical Theory and Computation
2022 | Journal article
Contributors: Fukal, Jiří; Zgarbová, Marie; Jurečka, Petr; Šebera, Jakub; Sychrovský, Vladimír
Source: Self-asserted source
Petr Jurecka

The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA

Journal of Computational Chemistry
2022 | Journal article
Contributors: Fukal, Jiř́ı; Buděš́ınsk̀y, Miloš; Páv, Ondřej; Jurečka, Petr; Zgarbová, Marie; Šebera, Jakub; Sychrovsk̀y, Vladiḿır
Source: Self-asserted source
Petr Jurecka

Conformational energies and equilibria of cyclic dinucleotides in vacuo and in solution: computational chemistry vs. NMR experiments

Physical Chemistry Chemical Physics
2021 | Journal article
Contributors: Gutten, Ondrej; Jurečka, Petr; Tehrani, Zahra Aliakbar; Buděš́ınsk̀y, Miloš; Řezáč, Jan; Ruĺıšek, Luboḿır
Source: Self-asserted source
Petr Jurecka

Z-DNA as a touchstone for additive empirical force fields and a refinement of the alpha/gamma DNA torsions for AMBER

Journal of Chemical Theory and Computation
2021 | Journal article
Contributors: Zgarbová, Marie; Sponer, Jiri; Jurečka, Petr
Source: Self-asserted source
Petr Jurecka

Toward accurate hydrogen bonds by scalable quantum Monte Carlo

Journal of Chemical Theory and Computation
2019 | Journal article
Contributors: Dubecky, Matus; Jurecka, Petr; Mitas, Lubos; Ditte, Matej; Fanta, Roman
Source: Self-asserted source
Petr Jurecka

A-to B-DNA transition in AMBER force fields and its coupling to sugar pucker

Journal of Chemical Theory and Computation
2018 | Journal article
Contributors: Zgarbová, Marie; Jurečka, Petr; Sponer, Jiri; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

RNA nanopatterning on graphene

2D Materials
2018 | Journal article
Contributors: Li, Q; Froning, JP; Pykal, M; Zhang, S; Wang, Z; Vondrák, M; Banáš, P; Čépe, K; Jurečka, P; Šponer, J et al.
Source: Self-asserted source
Petr Jurecka

RNA structural dynamics as captured by molecular simulations: a comprehensive overview

Chemical reviews
2018 | Journal article
Contributors: Sponer, Jiri; Bussi, Giovanni; Krepl, Miroslav; Banáš, Pavel; Bottaro, S; ro; Cunha, Richard A; Gil-Ley, Alej; ro; Pinamonti, Giovanni et al.
Source: Self-asserted source
Petr Jurecka

Adsorption of organic molecules to van der Waals materials: comparison of fluorographene and fluorographite with graphene and graphite

Journal of Chemical Theory and Computation
2017 | Journal article
Contributors: Karlicky, Frantisek; Otyepkova, Eva; Lo, Rabindranath; Pitonak, Michal; Jurecka, Petr; Pykal, Martin; Hobza, Pavel; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

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

Wiley Interdisciplinary Reviews: RNA
2017 | Journal article
Contributors: Šponer, Jiř́ı; Krepl, Miroslav; Banáš, Pavel; Kührová, Petra; Zgarbová, Marie; Jurečka, Petr; Havrila, Marek; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

Influence of BII backbone substates on DNA twist: a unified view and comparison of simulation and experiment for all 136 distinct tetranucleotide sequences

Journal of chemical information and modeling
2017 | Journal article
Contributors: Zgarbová, Marie; Jurecka, Petr; Lankas, Filip; Cheatham III, Thomas E; Sponer, Jiri; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

Mapping the chemical space of the RNA cleavage and its implications for ribozyme catalysis

The Journal of Physical Chemistry B
2017 | Journal article
Contributors: Mlynsky, Vojtech; Kuhrova, Petra; Jurečka, Petr; Sponer, Jiri; Otyepka, Michal; Banáš, Pavel
Source: Self-asserted source
Petr Jurecka

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

The Journal of Physical Chemistry B
2017 | Journal article
Contributors: Zgarbova, Marie; Jurečka, Petr; Banáš, Pavel; Havrila, Marek; Sponer, Jiri; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

Assessing the current state of amber force field modifications for DNA

Journal of chemical theory and computation
2016 | Journal article
Contributors: Galindo-Murillo, Rodrigo; Robertson, James C; Zgarbova, Marie; Sponer, Jiri; Otyepka, Michal; Jurecka, Petr; Cheatham III, Thomas E
Source: Self-asserted source
Petr Jurecka

Modelling of graphene functionalization

Physical Chemistry Chemical Physics
2016 | Journal article
Contributors: Pykal, Martin; Jurečka, Petr; Karlick̀y, František; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

Noncovalent interactions by quantum Monte Carlo

Chemical Reviews
2016 | Journal article
Contributors: Dubecky, Matus; Mitas, Lubos; Jurecka, Petr
Source: Self-asserted source
Petr Jurecka

On the use of molecular dynamics simulations for probing allostery through DNA

Biophysical journal
2016 | Journal article
Contributors: Dršata, Tomáš; Zgarbová, Marie; Jurečka, Petr; Šponer, Jiř́ı; Lankaš, Filip
Source: Self-asserted source
Petr Jurecka

Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals

Physical Chemistry Chemical Physics
2015 | Journal article
Contributors: Kocman, Mikuláš; Jurečka, Petr; Dubeck̀y, Matúš; Otyepka, Michal; Cho, Yeonchoo; Kim, Kwang S
Source: Self-asserted source
Petr Jurecka

Coarse-grain simulations of skin ceramide NS with newly derived parameters clarify structure of melted phase

The Journal of Physical Chemistry B
2015 | Journal article
Contributors: Sovova, Zofie; Berka, Karel; Otyepka, Michal; Jurecka, Petr
Source: Self-asserted source
Petr Jurecka

Extensions and applications of the A24 data set of accurate interaction energies

Physical Chemistry Chemical Physics
2015 | Journal article
Contributors: Řezáč, Jan; Dubeck̀y, Matúš; Jurečka, Petr; Hobza, Pavel
Source: Self-asserted source
Petr Jurecka

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

The Journal of Physical Chemistry B
2015 | Journal article
Contributors: Havrila, Marek; Zgarbová, Marie; Jurecka, Petr; Banas, Pavel; Krepl, Miroslav; Otyepka, Michal; Sponer, Jiri
Source: Self-asserted source
Petr Jurecka

Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with $ɛ$/$ζ$ Force Field Reparametrizations

The Journal of Physical Chemistry B
2015 | Journal article
Contributors: Mlýnský, Vojtěch; Kührová, Petra; Zgarbová, Marie; Jurečka, Petr; Walter, Nils G; Otyepka, Michal; Šponer, Jiř́ı; Banáš, Pavel
Source: Self-asserted source
Petr Jurecka

Refinement of the sugar--phosphate backbone torsion beta for AMBER force fields improves the description of Z-and B-DNA

Journal of chemical theory and computation
2015 | Journal article
Contributors: Zgarbová, Marie; Sponer, Jiri; Otyepka, Michal; Cheatham III, Thomas E; Galindo-Murillo, Rodrigo; Jurecka, Petr
Source: Self-asserted source
Petr Jurecka

Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields

Journal of computational chemistry
2015 | Journal article
Contributors: Zgarbová, Marie; Rosnik, Andreana M; Luque, F Javier; Curutchet, Carles; Jurečka, Petr
Source: Self-asserted source
Petr Jurecka

Base pair fraying in molecular dynamics simulations of DNA and RNA

Journal of chemical theory and computation
2014 | Journal article
Contributors: Zgarbová, Marie; Otyepka, Michal; Sponer, Jiri; Lankas, Filip; Jurecka, Petr
Source: Self-asserted source
Petr Jurecka

Electric quadrupole moment of graphene and its effect on intermolecular interactions

Physical Chemistry Chemical Physics
2014 | Journal article
Contributors: Kocman, Mikuláš; Pykal, Martin; Jurečka, Petr
Source: Self-asserted source
Petr Jurecka

Energies and 2′-hydroxyl group orientations of RNA backbone conformations. Benchmark CCSD (T)/CBS database, electronic analysis, and assessment of DFT methods and MD simulations

Journal of Chemical Theory and Computation
2014 | Journal article
Contributors: Mladek, Arnost; Banas, Pavel; Jurecka, Petr; Otyepka, Michal; Zgarbova, Marie; Sponer, Jiri
Source: Self-asserted source
Petr Jurecka

Mechanical model of DNA allostery

The journal of physical chemistry letters
2014 | Journal article
Contributors: Drsata, Tomas; Zgarbová, Marie; Špačková, Naďa; Jurečka, Petr; Sponer, Jiri; Lankas, Filip
Source: Self-asserted source
Petr Jurecka

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

Nucleic acids research
2014 | Journal article
Contributors: Dršata, Tomáš; Špačková, Naďa; Jurečka, Petr; Zgarbová, Marie; Šponer, Jiř́ı; Lankaš, Filip
Source: Self-asserted source
Petr Jurecka

Molecular dynamics simulations of nucleic acids. From tetranucleotides to the ribosome

The journal of physical chemistry letters
2014 | Journal article
Contributors: Šponer, Jiř́ı; Banáš, Pavel; Jurecka, Petr; Zgarbová, Marie; Kührová, Petra; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

Quantum Monte Carlo for noncovalent interactions: an efficient protocol attaining benchmark accuracy

Physical Chemistry Chemical Physics
2014 | Journal article
Contributors: Dubeck̀y, Matúš; Derian, René; Jurečka, Petr; Mitas, Lubos; Hobza, Pavel; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

Adsorption of small organic molecules on graphene

Journal of the American Chemical Society
2013 | Journal article
Contributors: Lazar, Petr; Karlicky, Frantisek; Jurecka, Petr; Kocman, Mikuláš; Otyepková, Eva; Šafářová, Klára; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

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

Physical Chemistry Chemical Physics
2013 | Journal article
Contributors: Mládek, Arnošt; Krepl, Miroslav; Svozil, Daniel; Čech, Petr; Otyepka, Michal; Banáš, Pavel; Zgarbova, Marie; Jurečka, Petr; Šponer, Jiř́ı
Source: Self-asserted source
Petr Jurecka

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

Methods
2013 | Journal article
Contributors: Šponer, Jiř́ı; Šponer, Judit E; Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

Lipid enhanced exfoliation for production of graphene nanosheets

The Journal of Physical Chemistry C
2013 | Journal article
Contributors: Pykal, Martin; Šafářová, Klára; Machalová Šišková, Karolína; Jurečka, Petr; Bourlinos, Athanasios B; Zbořil, Radek; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment

Biopolymers
2013 | Journal article
Contributors: Šponer, Jiř́ı; Šponer, Judit E; Mládek, Arnošt; Jurečka, Petr; Banáš, Pavel; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

Quantum Monte Carlo methods describe noncovalent interactions with subchemical accuracy

Journal of Chemical Theory and Computation
2013 | Journal article
Contributors: Dubecky, Matus; Jurecka, Petr; Derian, René; Hobza, Pavel; Otyepka, Michal; Mitas, Lubos
Source: Self-asserted source
Petr Jurecka

Toward improved description of DNA backbone: revisiting epsilon and zeta torsion force field parameters

Journal of chemical theory and computation
2013 | Journal article
Contributors: Zgarbová, Marie; Luque, F Javier; Sponer, Jiri; Cheatham III, Thomas E; Otyepka, Michal; Jurecka, Petr
Source: Self-asserted source
Petr Jurecka

A novel approach for deriving force field torsion angle parameters accounting for conformation-dependent solvation effects

Journal of chemical theory and computation
2012 | Journal article
Contributors: Zgarbova, Marie; Luque, F Javier; Sponer, Jiri; Otyepka, Michal; Jurecka, Petr
Source: Self-asserted source
Petr Jurecka

Can we accurately describe the structure of adenine tracts in B-DNA? Reference quantum-chemical computations reveal overstabilization of stacking by molecular mechanics

Journal of Chemical Theory and Computation
2012 | Journal article
Contributors: Banáš, Pavel; Mládek, Arnošt; Otyepka, Michal; Zgarbova, Marie; Jurečka, Petr; Svozil, Daniel; Lankaš, Filip; Šponer, Jiř́ı
Source: Self-asserted source
Petr Jurecka

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

Journal of chemical theory and computation
2012 | Journal article
Contributors: Krepl, Miroslav; Zgarbová, Marie; Stadlbauer, Petr; Otyepka, Michal; Banáš, Pavel; Koca, Jaroslav; Cheatham III, Thomas E; Jurecka, Petr; Sponer, Jiri
Source: Self-asserted source
Petr Jurecka

The DNA and RNA sugar--phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

Physical Chemistry Chemical Physics
2012 | Journal article
Contributors: Šponer, Jiř́ı; Mládek, Arnošt; Šponer, Judit E; Svozil, Daniel; Zgarbová, Marie; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

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

The Journal of Physical Chemistry A
2011 | Journal article
Contributors: Zgarbova, Marie; Jurecka, Petr; Banas, Pavel; Otyepka, Michal; Sponer, Judit E; Leontis, Neocles B; Zirbel, Craig L; Sponer, Jiri
Source: Self-asserted source
Petr Jurecka

Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles

Journal of chemical theory and computation
2011 | Journal article
Contributors: Zgarbová, Marie; Otyepka, Michal; Šponer, Jiří; Mládek, Arnošt; Banáš, Pavel; Cheatham III, Thomas E; Jurecka, Petr
Source: Self-asserted source
Petr Jurecka

Conformational Energies of DNA Sugar- Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics

Journal of Chemical Theory and Computation
2010 | Journal article
Contributors: Mladek, Arnost; Sponer, Judit E; Jurecka, Petr; Banas, Pavel; Otyepka, Michal; Svozil, Daniel; Sponer, Jiri
Source: Self-asserted source
Petr Jurecka

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations

Physical Chemistry Chemical Physics
2010 | Journal article
Contributors: Zgarbová, Marie; Otyepka, Michal; Šponer, Jiř́ı; Hobza, Pavel; Jurečka, Petr
Source: Self-asserted source
Petr Jurecka

On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes

ChemPhysChem
2010 | Journal article
Contributors: Kolář, Michal; Berka, Karel; Jurečka, Petr; Hobza, Pavel
Source: Self-asserted source
Petr Jurecka

Performance of molecular mechanics force fields for RNA simulations: stability of UUCG and GNRA hairpins

Journal of Chemical Theory and Computation
2010 | Journal article
Contributors: Banás, Pavel; Hollas, Daniel; Zgarbová, Marie; Jurecka, Petr; Orozco, Modesto; Cheatham III, Thomas E; Sponer, Jiri; Otyepka, Michal
Source: Self-asserted source
Petr Jurecka

Reference MP2/CBS and CCSD (T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2. 5, SCS (MI)-MP2, M06-2X, CBS (SCS-D) and force field descriptions

Physical Chemistry Chemical Physics
2010 | Journal article
Contributors: Morgado, Claudio A; Jurečka, Petr; Svozil, Daniel; Hobza, Pavel; Šponer, Jiř́ı
Source: Self-asserted source
Petr Jurecka
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Peer review (11 reviews for 6 publications/grants)

Review activity for ACS omega. (2)
Review activity for Journal of chemical information and modeling. (3)
Review activity for Journal of chemical physics. (1)
Review activity for Journal of chemical theory and computation : (1)
Review activity for The journal of physical chemistry letters. (1)
Review activity for The journal of physical chemistry. (3)
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