List of works - Andrea Amadei

A fast redox-induced switching mechanism in a conformationally controllable molecular thread in solution

scientific article published on 05 March 2010

A few key residues determine the high redox potential shift in azurin mutants.

scientific article published on 18 September 2015

A general theoretical model for electron transfer reactions in complex systems

scientific article published on 09 December 2011

A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells

scientific article published on 01 May 1999

A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy

scientific article published on 03 October 2018

A theoretical reappraisal of polylysine in the investigation of secondary structure sensitivity of infrared spectra

scientific article published on 07 March 2012

Aggregation of small peptides studied by molecular dynamics simulations

scientific article published on 01 December 2006

Analysis of infrared spectra of β-hairpin peptides as derived from molecular dynamics simulations

scientific article published on 26 September 2011

Can a synthetic thread act as an electrochemically switchable molecular device?

scientific article published on 19 June 2008

Characterization of electronic properties in complex molecular systems: modeling of a micropolarity probe

scientific article published in February 2010

Charge transfer equilibria of aqueous single stranded DNA.

scientific article published on 28 October 2009

Conformational and Electronic Properties of a Microperoxidase in Aqueous Solution: A Computational Study

scientific article published on 01 April 2005

Conformational fluctuations and electronic properties in myoglobin.

scientific article published in May 2004

Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.

scientific article

Effect of High Exogenous Electric Pulses on Protein Conformation: Myoglobin as a Case Study

scientific article published on 15 February 2013

Effects of local electric fields on the redox free energy of single stranded DNA

scientific article published on 23 December 2010

Entropy-energy balance in base catalyzed keto-enol interconversion: A joint theoretical and experimental investigation

Essential dynamics for the study of microstructures in liquids

scientific article

Essential dynamics of proteins

scientific article (publication date: December 1993)

Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin

scientific article published on June 2004

Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory

scientific article published on 14 September 2018

Folding propensity and biological activity of peptides: New insights from conformational properties of a novel peptide derived from Vitreoscilla haemoglobin

scientific article published on 01 September 2007

Free-energy profile for CO binding to separated chains of human and Trematomus newnesi hemoglobin: insights from molecular dynamics simulations and perturbed matrix method

scientific article published in May 2010

Ground and excited electronic state thermodynamics of aqueous carbon monoxide: a theoretical study

scientific article published on 01 March 2005

How the Reorganization Free Energy Affects the Reduction Potential of Structurally Homologous Cytochromes

scientific article published on 14 April 2014

Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations

scientific article published on 01 November 1998

In silico characterization of protein partial molecular volumes and hydration shells.

scientific article published on 9 November 2015

Inclusion of cybotactic effect in the theoretical modeling of absorption spectra of liquid-state systems with perturbed matrix method and molecular dynamics simulations: the UV–Vis absorption spectrum of para-nitroaniline as a case study

article

Kinetics of carbon monoxide migration and binding in solvated myoglobin as revealed by molecular dynamics simulations and quantum mechanical calculations

scientific article published in December 2009

Kinetics of carbon monoxide migration and binding in solvated neuroglobin as revealed by molecular dynamics simulations and quantum mechanical calculations

scientific article published on 18 February 2011

Modeling amino-acid side chain infrared spectra: the case of carboxylic residues

scientific article published on 20 January 2020

Modeling of Chemical Reactions in Micelle: Water-Mediated Keto–Enol Interconversion As a Case Study

scientific article published on 07 June 2011

Modeling triplet flavin-indole electron transfer and interradical dipolar interaction: a perturbative approach

Modelling vibrational relaxation in complex molecular systems

scientific article published on 01 September 2019

Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities

scientific article published on 22 April 2005

Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water

article

Molecular mechanisms of activation in CDK2.

scientific article

Monitoring the folding kinetics of a β-hairpin by time-resolved IR spectroscopy in silico.

scientific article

New insight into the IR-spectra/structure relationship in amyloid fibrils: a theoretical study on a prion peptide.

scientific article published on 8 July 2011

On the effect of a point mutation on the reactivity of CuZn superoxide dismutase: a theoretical study

scientific article published on 01 April 2006

Prediction of protein conformational freedom from distance constraints

scientific article published on 01 October 1997

Protein Folding Pathways Revealed by Essential Dynamics Sampling

scientific article

Simulation of the amide I infrared spectrum in photoinduced peptide folding/unfolding transitions

scientific article published on 03 October 2013

Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation

scientific article published on 12 August 2008

Structural rearrangements of the two domains of Azotobacter vinelandii rhodanese upon sulfane sulfur release: essential molecular dynamics, 15N NMR relaxation and deuterium exchange on the uniformly labeled protein

scientific article

Structural, thermodynamic, and kinetic properties of Gramicidin analogue GS6 studied by molecular dynamics simulations and statistical mechanics

scientific article published in December 2009

Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace.

scientific article published in July 1995

The Reversible Opening of Water Channels in Cytochrome c Modulates the Heme Iron Reduction Potential

scientific article published on 09 August 2012

The conformation of constitutive DNA interaction sites for eukaryotic DNA topoisomerase I on intrinsically curved DNAs

scientific article published on 01 December 1991

The effects of the L29F mutation on the ligand migration kinetics in crystallized myoglobin as revealed by molecular dynamics simulations

scientific article published on 22 December 2010

The essential dynamics of thermolysin: Confirmation of the hinge-bending motion and comparison of simulations in vacuum and water

article

The kinetics of ligand migration in crystallized myoglobin as revealed by molecular dynamics simulations.

scientific article

Theoretical characterisation of the electronic excitation in liquid water

scientific article published on 01 January 2005

Theoretical characterization of alpha-helix and beta-hairpin folding kinetics.

scientific article published in October 2005

Theoretical characterization of electronic states in interacting chemical systems

scientific article published on 01 February 2009

Theoretical characterization of temperature and density dependence of liquid water electronic excitation energy: comparison with recent experimental data.

scientific article

Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: explicit treatment of the vibronic transitions.

scientific article published in April 2014

Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: the vertical transition approximation.

scientific article

Theoretical modeling of enzyme reactions: the thermodynamics of formation of compound 0 in horseradish peroxidase

scientific article published on 21 February 2008

Theoretical modeling of the valence UV spectra of 1,2,3-triazine and uracil in solution.

scientific article published on 24 February 2006

Theoretical modeling of vibroelectronic quantum states in complex molecular systems: solvated carbon monoxide, a test case

scientific article published on 01 March 2005

Theoretical study of intramolecular charge transfer in π-conjugated oligomers

Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solution.

scientific article

Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations.

scientific article published on 29 January 2010

Theoretical-computational modelling of the temperature dependence of the folding-unfolding thermodynamics and kinetics: the case of a Trp-cage

scientific article published on 01 October 2019

Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water.

scientific article published in May 2005

Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties

scientific article published on 14 May 2018

List of works by Andrea Amadei

A fast redox-induced switching mechanism in a conformationally controllable molecular thread in solution

A few key residues determine the high redox potential shift in azurin mutants.

A general theoretical model for electron transfer reactions in complex systems

A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells

A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy

A theoretical reappraisal of polylysine in the investigation of secondary structure sensitivity of infrared spectra

Aggregation of small peptides studied by molecular dynamics simulations

Analysis of infrared spectra of β-hairpin peptides as derived from molecular dynamics simulations

Can a synthetic thread act as an electrochemically switchable molecular device?

Characterization of electronic properties in complex molecular systems: modeling of a micropolarity probe

Charge transfer equilibria of aqueous single stranded DNA.

Conformational and Electronic Properties of a Microperoxidase in Aqueous Solution: A Computational Study

Conformational fluctuations and electronic properties in myoglobin.

Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.

Effect of High Exogenous Electric Pulses on Protein Conformation: Myoglobin as a Case Study

Effects of local electric fields on the redox free energy of single stranded DNA

Entropy-energy balance in base catalyzed keto-enol interconversion: A joint theoretical and experimental investigation

Essential dynamics for the study of microstructures in liquids

Essential dynamics of proteins

Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin

Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory

Folding propensity and biological activity of peptides: New insights from conformational properties of a novel peptide derived from Vitreoscilla haemoglobin

Free-energy profile for CO binding to separated chains of human and Trematomus newnesi hemoglobin: insights from molecular dynamics simulations and perturbed matrix method

Ground and excited electronic state thermodynamics of aqueous carbon monoxide: a theoretical study

How the Reorganization Free Energy Affects the Reduction Potential of Structurally Homologous Cytochromes

Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations

In silico characterization of protein partial molecular volumes and hydration shells.

Inclusion of cybotactic effect in the theoretical modeling of absorption spectra of liquid-state systems with perturbed matrix method and molecular dynamics simulations: the UV–Vis absorption spectrum of para-nitroaniline as a case study

Kinetics of carbon monoxide migration and binding in solvated myoglobin as revealed by molecular dynamics simulations and quantum mechanical calculations

Kinetics of carbon monoxide migration and binding in solvated neuroglobin as revealed by molecular dynamics simulations and quantum mechanical calculations

Modeling amino-acid side chain infrared spectra: the case of carboxylic residues

Modeling of Chemical Reactions in Micelle: Water-Mediated Keto–Enol Interconversion As a Case Study

Modeling triplet flavin-indole electron transfer and interradical dipolar interaction: a perturbative approach

Modelling vibrational relaxation in complex molecular systems

Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities

Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water

Molecular mechanisms of activation in CDK2.

Monitoring the folding kinetics of a β-hairpin by time-resolved IR spectroscopy in silico.

New insight into the IR-spectra/structure relationship in amyloid fibrils: a theoretical study on a prion peptide.

On the effect of a point mutation on the reactivity of CuZn superoxide dismutase: a theoretical study

Prediction of protein conformational freedom from distance constraints

Protein Folding Pathways Revealed by Essential Dynamics Sampling

Simulation of the amide I infrared spectrum in photoinduced peptide folding/unfolding transitions

Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation

Structural rearrangements of the two domains of Azotobacter vinelandii rhodanese upon sulfane sulfur release: essential molecular dynamics, 15N NMR relaxation and deuterium exchange on the uniformly labeled protein

Structural, thermodynamic, and kinetic properties of Gramicidin analogue GS6 studied by molecular dynamics simulations and statistical mechanics

Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace.

The Reversible Opening of Water Channels in Cytochrome c Modulates the Heme Iron Reduction Potential

The conformation of constitutive DNA interaction sites for eukaryotic DNA topoisomerase I on intrinsically curved DNAs

The effects of the L29F mutation on the ligand migration kinetics in crystallized myoglobin as revealed by molecular dynamics simulations

The essential dynamics of thermolysin: Confirmation of the hinge-bending motion and comparison of simulations in vacuum and water

The kinetics of ligand migration in crystallized myoglobin as revealed by molecular dynamics simulations.

Theoretical characterisation of the electronic excitation in liquid water

Theoretical characterization of alpha-helix and beta-hairpin folding kinetics.

Theoretical characterization of electronic states in interacting chemical systems

Theoretical characterization of temperature and density dependence of liquid water electronic excitation energy: comparison with recent experimental data.

Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: explicit treatment of the vibronic transitions.

Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: the vertical transition approximation.

Theoretical modeling of enzyme reactions: the thermodynamics of formation of compound 0 in horseradish peroxidase

Theoretical modeling of the valence UV spectra of 1,2,3-triazine and uracil in solution.

Theoretical modeling of vibroelectronic quantum states in complex molecular systems: solvated carbon monoxide, a test case

Theoretical study of intramolecular charge transfer in π-conjugated oligomers

Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solution.

Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations.

Theoretical-computational modelling of the temperature dependence of the folding-unfolding thermodynamics and kinetics: the case of a Trp-cage

Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water.

Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties