P. Banáš

发表

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

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

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.

J. Šponer, M. Otyepka, P. Banáš, 2014, Journal of chemical theory and computation.

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

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

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.

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

J. Šponer, T. Cheatham, M. Otyepka, 2011, Journal of chemical theory and computation.

Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact.

M. Otyepka, P. Banáš, Petra Florová, 2010, 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.

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.

Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration.

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2012, The journal of physical chemistry. B.

Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies.

J. Šponer, G. Bussi, M. Otyepka, 2016, Biochimica et biophysica acta. General subjects.

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

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

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

J. Šponer, G. Bussi, M. Otyepka, 2017, Journal of chemical theory and computation.

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

J. Šponer, J. Koča, G. Bussi, 2015, Nucleic acids research.

Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study.

J. Šponer, J. Wedekind, M. Otyepka, 2012, The journal of physical chemistry. B.

Molecular Mechanism of preQ 1 Riboswitch Action: A Molecular Dynamics Study

J. Šponer, J. Wedekind, M. Otyepka, 2012 .

W-RESP: Well-Restrained Electrostatic Potential Derived Charges. Revisiting the Charge Derivation Model

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

Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

J. Šponer, G. Bussi, M. Otyepka, 2020, bioRxiv.

Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis.

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

Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes

J. Šponer, M. Otyepka, P. Banáš, 2019, Nucleic acids research.

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

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

Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations.

J. Šponer, M. Otyepka, P. Banáš, 2014, Journal of chemical theory and computation.

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.

Computer Aided Development of Nucleic Acid Applications in Nanotechnologies.

J. Šponer, M. Otyepka, P. Banáš, 2022, Small.

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.

Reactivity of Fluorographene: A Facile Way toward Graphene Derivatives.

M. Dubecký, M. Otyepka, P. Banáš, 2015, The journal of physical chemistry letters.

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.

Yuji Nagata, Michal Otyepka, Zbynek Prokop, 2009, Nature chemical biology.

Ion Interactions across Graphene in Electrolyte Aqueous Solutions

M. Otyepka, P. Banáš, M. Langer, 2019, The Journal of Physical Chemistry C.

The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2015, Physical chemistry chemical physics : PCCP.

W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model.

J. Šponer, M. Otyepka, P. Banáš, 2021, Journal of chemical theory and computation.

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.

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.

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

Giovanni Bussi, Michal Otyepka, Sandro Bottaro, 2016, Journal of chemical theory and computation.

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.

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

Michal Otyepka, Arnošt Mládek, Petr Jurečka, 2013, Methods.

Computer Folding of RNA Tetraloops? Are We There Yet?

Michal Otyepka, Robert B Best, Pavel Banáš, 2013, Journal of chemical theory and computation.

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

Daniel Svozil, Michal Otyepka, Arnošt Mládek, 2012, Physical chemistry chemical physics : PCCP.

Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics.

Daniel Svozil, Michal Otyepka, Arnošt Mládek, 2012, Journal of chemical theory and computation.

Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs.

K. Réblová, J. Šponer, M. Otyepka, 2011, Journal of Chemical Theory and Computation.

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.

Michal Otyepka, Modesto Orozco, Thomas E. Cheatham, 2010, Journal of chemical theory and computation.

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.

K. Réblová, J. Šponer, N. Walter, 2010, The journal of physical chemistry. B.

Click and Detect: Versatile Ampicillin Aptasensor Enabled by Click Chemistry on a Graphene-Alkyne Derivative.

M. Otyepka, P. Banáš, A. Bakandritsos, 2023, Small.

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

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

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.

110 Refinement of force field torsion parameters for nucleic acids based on inclusion of conformation-dependent solvation effects

F. J. Luque, J. Šponer, T. Cheatham, 2013 .

Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications.

J. Šponer, G. Bussi, M. Otyepka, 2022, Journal of chemical theory and computation.

Towards Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Corrections

J. Šponer, G. Bussi, M. Otyepka, 2021, 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.

Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

J. Šponer, G. Bussi, M. Otyepka, 2020, bioRxiv.

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.

Fitting Corrections to an RNA Force Field Using Experimental Data.

J. Šponer, Sandro Bottaro, K. Lindorff-Larsen, 2019, Journal of chemical theory and computation.

Local-to-global signal transduction at the core of the Mn2+ sensing riboswitch

J. Šponer, N. Walter, P. Banáš, 2019, bioRxiv.

RNA nanopatterning on graphene

M. Otyepka, Shaohua Zhang, P. Banáš, 2018 .

Chemical feasibility of the general acid/base mechanism of glmS ribozyme self‐cleavage

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2015, Biopolymers.

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics.

Michal Otyepka, Pavel Hobza, Vojtěch Spiwok, 2015, Journal of chemical theory and computation.

Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ force field reparametrizations.

J. Šponer, N. Walter, M. Otyepka, 2015, The journal of physical chemistry. B.

Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.

K. Réblová, J. Šponer, N. Walter, 2015, Physical chemistry chemical physics : PCCP.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

J. Šponer, N. Walter, M. Otyepka, 2014, RNA.

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme.

Adrian J Mulholland, Michal Otyepka, Pavel Banáš, 2014, Journal of chemical theory and computation.

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

J. Šponer, M. Otyepka, P. Banáš, 2010 .

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2012, Nucleic Acids Res..

Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.

J. Šponer, N. Walter, M. Otyepka, 2009, Methods.

Theoretical studies on the intermolecular interactions of potentially primordial base-pair analogues.

B. Sumpter, Á. Vázquez-Mayagoitia, M. Otyepka, 2010, Chemistry.

Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine

J. Šponer, R. Improta, P. Banáš, 2021, International Journal of Biological Macromolecules.

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

Jaroslav Koca, Michal Otyepka, Jirí Damborský, 2006, BMC Bioinformatics.

Promoting transparency and reproducibility in enhanced molecular simulations

Jakub Rydzewski, Toni Giorgino, Massimiliano Bonomi, 2019, Nature Methods.

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2013, Journal of Cheminformatics.

Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles

Michal Otyepka, Jirí Damborský, Martin Petrek, 2007, Biotechnology journal.

Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods

Alessandra Magistrato, Michal Otyepka, Jiří Damborský, 2008, Proteins.

Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects.

J. Šponer, P. Banáš, H. Kruse, 2018, Journal of chemical theory and computation.

Variability of C–F Bonds Governs the Formation of Specific Structural Motifs in Fluorinated Graphenes

M. Otyepka, P. Banáš, R. Langer, 2019, The Journal of Physical Chemistry C.

Anatomy of enzyme channels

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2014, BMC Bioinformatics.

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

Michal Otyepka, Arnošt Mládek, Petr Jurečka, 2013, Biopolymers.

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility.

J. Šponer, N. Walter, M. Otyepka, 2008, The journal of physical chemistry. B.

Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.

J. Šponer, N. Walter, M. Otyepka, 2010, The journal of physical chemistry. B.

QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.

J. Šponer, N. Walter, M. Otyepka, 2011, The journal of physical chemistry. B.

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.

Craig L. Zirbel, J. Šponer, N. Leontis, 2011, The journal of physical chemistry. A.

Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes

J. Šponer, M. Otyepka, P. Banáš, 2023, J. Chem. Inf. Model..

Free Energy Landscape of GAGA and UUCG RNA Tetraloops.

Giovanni Bussi, Sandro Bottaro, Pavel Banáš, 2016, The journal of physical chemistry letters.

Exponential repulsion improves structural predictability of molecular docking

Karel Berka, Michal Otyepka, Václav Bazgier, 2016, J. Comput. Chem..

The nature of high surface energy sites in graphene and graphite

M. Otyepka, P. Banáš, R. Zbořil, 2014 .

Molecular Insights from Theoretical Calculations Explain the Differences in Affinity and Diffusion of Airborne Contaminants on Surfaces of hBN and Graphene

M. Otyepka, P. Banáš, K. Čépe, 2021 .

Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling

Michal Otyepka, Jirí Damborský, Martin Petrek, 2006, J. Comput. Aided Mol. Des..

Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch

J. Šponer, N. Walter, P. Banáš, 2019, Nature Communications.

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

J. Koča, J. Damborský, M. Otyepka, 2006, BMC Bioinformatics.

Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies.

J. Šponer, G. Bussi, M. Otyepka, 2016, Biochimica et biophysica acta. General subjects.

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

J. Koča, J. Damborský, M. Otyepka, 2006, BMC Bioinformatics.

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.

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.

Craig L. Zirbel, N. Leontis, M. Otyepka, 2011, The journal of physical chemistry. A.

Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs.

K. Réblová, J. Šponer, M. Otyepka, 2011, Journal of chemical theory and computation.

Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations.

J. Šponer, M. Otyepka, P. Banáš, 2014, Journal of chemical theory and computation.