List of works - Edina Rosta

A Dynamic and Responsive Host in Action: Light-Controlled Molecular Encapsulation

scientific article published on 28 October 2016

Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution

scientific article published on 16 April 2008

Advances in methods and algorithms in a modern quantum chemistry program package.

scientific article

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

article

Anomalously Large Spectral Shifts near the Quantum Tunnelling Limit in Plasmonic Rulers with Subatomic Resolution

scientific article published on 19 February 2019

Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

scientific article

Calcium inhibition of ribonuclease H1 two-metal ion catalysis

scientific article

Calculating Kinetic Rates and Membrane Permeability from Biased Simulations

article

Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations

scientific article

Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.

scientific article

Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

scientific article published on 14 February 2020

Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers

scientific article published on 20 June 2016

Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics

scientific article published on 23 February 2022

Controlling the structure and photophysics of fluorophore dimers using multiple cucurbit[8]uril clampings

scientific article

Correlation functions, mean first passage times, and the Kemeny constant

scientific article published on 01 March 2020

Cucurbit[7]uril as a Supramolecular Artificial Enzyme for Diels-Alder Reactions.

scientific article

Cucurbit[8]uril-mediated pseudo[2,3]rotaxanes

scientific article published on 01 October 2019

Deviation from the anti-Markovnikov rule: a computational study of the regio- and stereoselectivity of diene hydroboration reactions

Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase

scientific article published on 14 October 2014

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling

scientific article published on 11 July 2018

Divergence from the classical hydroboration reactivity; boron containing materials through a hydroboration cascade of small cyclic dienes

article by Anna Andreou et al published 1 November 2015 in Chemical Science

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations.

scientific article published on 23 October 2017

Efficient Irreversible Monte Carlo Samplers

scientific article published on 17 March 2020

Error and efficiency of replica exchange molecular dynamics simulations

scientific article published on October 2009

Error and efficiency of simulated tempering simulations

scientific article

Exploring the role of the 5-substituent for the intrinsic fluorescence of 5-aryl and 5-heteroaryl uracil nucleotides: a systematic study

scientific article

Extending the mirror neuron system model, I. Audible actions and invisible grasps

scientific article

Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model

article

Gas-phase structures reflect the pain-relief potency of enkephalin peptides

scientific article published on 01 October 2019

Geometry and electronic structure of bis(tetrahydridoborato)bis(cyclopentadienyl)zirconium(IV)

Human DHEA sulfation requires direct interaction between PAPS synthase 2 and DHEA sulfotransferase SULT2A1.

scientific article

Inhibiting Analyte Theft in Surface-Enhanced Raman Spectroscopy Substrates: Subnanomolar Quantitative Drug Detection

scientific article published on 01 November 2019

Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations.

scientific article published on 13 November 2017

Light-Regulated Molecular Trafficking in a Synthetic Water-Soluble Host

scientific article published on 28 April 2016

Limiting relaxation times from Markov state models

scientific article published on 01 August 2018

MST2-RASSF protein-protein interactions through SARAH domains

scientific article published on 5 October 2015

Markov Models of Molecular Kinetics

scientific article published on 01 November 2019

Mean first passage times in variational coarse graining using Markov state models

scientific article published on 01 April 2019

Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design

scientific article published on 06 September 2021

Modular supramolecular dimerization of optically tunable extended aryl viologens

scientific article published on 12 August 2019

Modulating the oxidation of cucurbit[n]urils

scientific article published on 11 January 2017

Molecular Vibration Explorer: an Online Database and Toolbox for Surface-Enhanced Frequency Conversion and Infrared and Raman Spectroscopy

scientific article published in 2022

Molecular mechanisms of asymmetric RAF dimer activation

scientific article

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

scientific article

On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions

scientific article published on 29 March 2012

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution

scientific article published on 29 February 2008

On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins

scientific article

On unjustifiably misrepresenting the EVB approach while simultaneously adopting it

scientific article published on August 2009

Organocatalytic Access to a cis-Cyclopentyl-γ-amino Acid: An Intriguing Model of Selectivity and Formation of a Stable 10/12-Helix from the Corresponding γ/α-Peptide

scientific article published on 23 December 2019

Peptide dimerization-dissociation rates from replica exchange molecular dynamics

scientific article

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation

scientific article published on 8 December 2015

Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis

scientific article published on 17 March 2021

Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme

scientific article

Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations

scientific article published on 29 September 2018

Room-Temperature Optical Picocavities below 1 nm3 Accessing Single-Atom Geometries

article

SARAH Domain-Mediated MST2-RASSF Dimeric Interactions.

scientific article published on 7 October 2016

Simulated tempering with irreversible Gibbs sampling techniques

scientific article published on 01 December 2020

Single-molecule strong coupling at room temperature in plasmonic nanocavities

scientific article

Smart supramolecular sensing with cucurbit[n]urils: probing hydrogen bonding with SERS.

scientific article published on 21 September 2017

Spectroscopic Evidence for Peptide-Bond-Selective Ultraviolet Photodissociation

scientific article published on 19 December 2019

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states ⬇️

scientific article

Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases ⬇️

scientific article published on 14 October 2016

Structural basis of second-generation HIV integrase inhibitor action and viral resistance

scientific article

THE MIRROR SYSTEM HYPOTHESIS: FROM A MACAQUE-LIKE MIRROR SYSTEM TO IMITATION

The differential impact of PAPS synthase isoforms on DHEAS may be explained by an isoform-specific interaction of SULT2A1 with PAPSS2, but not PAPSS1

Theoretical Study of the Mechanism of the Hydride Transfer between Ferredoxin–NADP+ Reductase and NADP+: The Role of Tyr303

scientific article published in 2012

Thermostat artifacts in replica exchange molecular dynamics simulations

scientific article published on January 2009

Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions

scientific article

Tracking Nanoelectrochemistry Using Individual Plasmonic Nanocavities.

scientific article

Turning Cucurbit[8]uril into a Supramolecular Nanoreactor for Asymmetric Catalysis

Turning Cucurbit[8]uril into a Supramolecular Nanoreactor for Asymmetric Catalysis.

scientific article published on 7 September 2015

Two-body zeroth order Hamiltonians in multireference perturbation theory: The APSG reference state

article by Edina Rosta & Péter R. Surján published 15 January 2002 in Journal of Chemical Physics

Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation

scientific article published on 09 March 2016

Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases

scientific article published in October 2006

List of works by Edina Rosta

A Dynamic and Responsive Host in Action: Light-Controlled Molecular Encapsulation

Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Anomalously Large Spectral Shifts near the Quantum Tunnelling Limit in Plasmonic Rulers with Subatomic Resolution

Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

Calcium inhibition of ribonuclease H1 two-metal ion catalysis

Calculating Kinetic Rates and Membrane Permeability from Biased Simulations

Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations

Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.

Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers

Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics

Controlling the structure and photophysics of fluorophore dimers using multiple cucurbit[8]uril clampings

Correlation functions, mean first passage times, and the Kemeny constant

Cucurbit[7]uril as a Supramolecular Artificial Enzyme for Diels-Alder Reactions.

Cucurbit[8]uril-mediated pseudo[2,3]rotaxanes

Deviation from the anti-Markovnikov rule: a computational study of the regio- and stereoselectivity of diene hydroboration reactions

Deviation from the anti-Markovnikov rule: a computational study of the regio- and stereoselectivity of diene hydroboration reactions

Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling

Divergence from the classical hydroboration reactivity; boron containing materials through a hydroboration cascade of small cyclic dienes

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations.

Efficient Irreversible Monte Carlo Samplers

Error and efficiency of replica exchange molecular dynamics simulations

Error and efficiency of simulated tempering simulations

Exploring the role of the 5-substituent for the intrinsic fluorescence of 5-aryl and 5-heteroaryl uracil nucleotides: a systematic study

Extending the mirror neuron system model, I. Audible actions and invisible grasps

Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model

Gas-phase structures reflect the pain-relief potency of enkephalin peptides

Geometry and electronic structure of bis(tetrahydridoborato)bis(cyclopentadienyl)zirconium(IV)

Human DHEA sulfation requires direct interaction between PAPS synthase 2 and DHEA sulfotransferase SULT2A1.

Inhibiting Analyte Theft in Surface-Enhanced Raman Spectroscopy Substrates: Subnanomolar Quantitative Drug Detection

Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations.

Light-Regulated Molecular Trafficking in a Synthetic Water-Soluble Host

Limiting relaxation times from Markov state models

MST2-RASSF protein-protein interactions through SARAH domains

Markov Models of Molecular Kinetics

Mean first passage times in variational coarse graining using Markov state models

Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design

Modular supramolecular dimerization of optically tunable extended aryl viologens

Modulating the oxidation of cucurbit[n]urils

Molecular Vibration Explorer: an Online Database and Toolbox for Surface-Enhanced Frequency Conversion and Infrared and Raman Spectroscopy

Molecular mechanisms of asymmetric RAF dimer activation

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution

On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins

On unjustifiably misrepresenting the EVB approach while simultaneously adopting it

Organocatalytic Access to a cis-Cyclopentyl-γ-amino Acid: An Intriguing Model of Selectivity and Formation of a Stable 10/12-Helix from the Corresponding γ/α-Peptide

Peptide dimerization-dissociation rates from replica exchange molecular dynamics

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation

Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis

Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme

Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations

Room-Temperature Optical Picocavities below 1 nm3 Accessing Single-Atom Geometries

SARAH Domain-Mediated MST2-RASSF Dimeric Interactions.

Simulated tempering with irreversible Gibbs sampling techniques

Single-molecule strong coupling at room temperature in plasmonic nanocavities

Smart supramolecular sensing with cucurbit[n]urils: probing hydrogen bonding with SERS.

Spectroscopic Evidence for Peptide-Bond-Selective Ultraviolet Photodissociation

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states ⬇️

Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases ⬇️

Structural basis of second-generation HIV integrase inhibitor action and viral resistance

THE MIRROR SYSTEM HYPOTHESIS: FROM A MACAQUE-LIKE MIRROR SYSTEM TO IMITATION

The differential impact of PAPS synthase isoforms on DHEAS may be explained by an isoform-specific interaction of SULT2A1 with PAPSS2, but not PAPSS1

Theoretical Study of the Mechanism of the Hydride Transfer between Ferredoxin–NADP+ Reductase and NADP+: The Role of Tyr303

Thermostat artifacts in replica exchange molecular dynamics simulations

Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions

Tracking Nanoelectrochemistry Using Individual Plasmonic Nanocavities.

Turning Cucurbit[8]uril into a Supramolecular Nanoreactor for Asymmetric Catalysis

Turning Cucurbit[8]uril into a Supramolecular Nanoreactor for Asymmetric Catalysis.

Two-body zeroth order Hamiltonians in multireference perturbation theory: The APSG reference state

Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation

Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases