List of works - Pavel Banáš

Anatomy of enzyme channels

scientific article

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

article

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

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

scientific article published on 6 June 2012

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

scientific article published on October 2015

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

scientific article published on April 2014

Computer Folding of RNA Tetraloops? Are We There Yet?

scientific article published on 7 March 2013

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

article by Arnošt Mládek et al published 14 December 2010 in Journal of Chemical Theory and Computation

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

scientific article published on 19 December 2019

Correction to “Free Energy Landscape of GAGA and UUCG RNA Tetraloops”

scientific article published on 19 March 2018

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

scientific article

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

article

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

scientific article published on 22 November 2013

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

article

Exponential repulsion improves structural predictability of molecular docking

scientific article published on 13 September 2016

Fitting Corrections to an RNA Force Field Using Experimental Data

scientific article published on 23 May 2019

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

scientific article

Free Energy Landscape of GAGA and UUCG RNA Tetraloops ⬇️

scientific article published on 23 September 2016

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

scientific article published on 3 October 2015

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

scientific article published on 10 November 2016

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

scientific article published on 07 June 2013

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

scientific article published on 02 April 2019

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

scientific article published on August 2015

Interplay between Ethanol Adsorption to High-Energy Sites and Clustering on Graphene and Graphite Alters the Measured Isosteric Adsorption Enthalpies

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

scientific article published on 12 December 2018

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

scientific article published on 20 September 2019

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

scientific article (publication date: 16 August 2013)

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

scientific article published on 8 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 dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

scientific article published on 24 October 2014

Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study

scientific article published on 12 October 2012

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

scientific article published in June 2013

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

article

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

scientific article published on 14 March 2017

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

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

scientific article published on 8 November 2011

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

scientific article published on 3 January 2018

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

scientific article published on 5 March 2015

Reactivity of Fluorographene: A Facile Way toward Graphene Derivatives

scientific article published on 2 April 2015

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

scientific article

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

scientific article published on 02 August 2011

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

scientific article published on 9 August 2012

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

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

scientific article published on 16 October 2012

The nature of high surface energy sites in graphene and graphite

scholarly article in Carbon, vol. 73, July 2014

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

scientific article published on 01 April 2022

Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18INK4c

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

scientific article published on 20 November 2020

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

scientific article published on 5 August 2011

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

scientific article published on 17 May 2021

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

scientific article published on February 2015

List of works by Pavel Banáš

Anatomy of enzyme channels

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

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

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

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

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

Computer Folding of RNA Tetraloops? Are We There Yet?

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

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

Correction to “Free Energy Landscape of GAGA and UUCG RNA Tetraloops”

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

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

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

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

Exponential repulsion improves structural predictability of molecular docking

Fitting Corrections to an RNA Force Field Using Experimental Data

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

Free Energy Landscape of GAGA and UUCG RNA Tetraloops ⬇️

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

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

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

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

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

Interplay between Ethanol Adsorption to High-Energy Sites and Clustering on Graphene and Graphite Alters the Measured Isosteric Adsorption Enthalpies

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

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

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

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

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

Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study

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

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

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

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

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

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

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

Reactivity of Fluorographene: A Facile Way toward Graphene Derivatives

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

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

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

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

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

The nature of high surface energy sites in graphene and graphite

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

Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18INK4c

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

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

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

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