I. Daidone

发表

Mechanism of DNA recognition by the restriction enzyme EcoRV.

Isabella Daidone, Jeremy C. Smith, Mai Zahran, 2010, Journal of molecular biology.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

John A. Gunnels, Julie C. Mitchell, Matthew B. Baker, 2020, ChemRxiv.

Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations.

Jeremy C. Smith, I. Daidone, Lipi Thukral, 2009, Journal of the American Chemical Society.

Inhibitor Binding Influences the Protonation State of Histidines in SARS-CoV-2 Main Protease

Jerry M. Parks, Jeremy C. Smith, Callum J. Dickson, 2020, bioRxiv.

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

M. Brunori, B. Vallone, A. Amadei, 2005, Biophysical journal.

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

Jeremy C. Smith, J. Chodera, F. Noé, 2011, Proceedings of the National Academy of Sciences.

Configurational subdiffusion of peptides: a network study.

Isabella Daidone, Jeremy C. Smith, Jeremy C Smith, 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

Computational investigation of the electron transfer complex between neuroglobin and cytochrome c

I. Daidone, C. Bortolotti, M. Pignataro, 2017 .

A general statistical mechanical approach for modeling redox thermodynamics: the reaction and reorganization free energies

A. Amadei, I. Daidone, C. Bortolotti, 2013 .

β-Structure within the Denatured State of the Helical Protein Domain BBL.

I. Daidone, H. Neuweiler, Lipi Thukral, 2015, Journal of molecular biology.

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

A. Amadei, M. D’Abramo, I. Daidone, 2014, Physical chemistry chemical physics : PCCP.

Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde

A. Amadei, M. D’Abramo, I. Daidone, 2006 .

The reversible opening of water channels in cytochrome c modulates the heme iron reduction potential.

A. Amadei, I. Daidone, C. Bortolotti, 2012, Journal of the American Chemical Society.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

John A. Gunnels, Julie C. Mitchell, Matthew B. Baker, 2020, Journal of chemical information and modeling.

Conformational Change in the Mechanism of Inclusion of Ketoprofen in β-Cyclodextrin: NMR Spectroscopy, Ab Initio Calculations, Molecular Dynamics Simulations, and Photoreactivity.

I. Daidone, M. Paci, E. Bodo, 2016, The journal of physical chemistry. B.

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

A. Amadei, A. di Nola, M. Anselmi, 2011, The journal of physical chemistry. B.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

Duncan Poole, John A. Gunnels, Arvind Ramanathan, 2020, J. Chem. Inf. Model..

Photophysical and Computational Insights into Ag(I) Complexation of Porphyrinic Covalent Cages Equipped with Triazoles-Incorporating Linkers

I. Daidone, L. Zanetti-Polzi, B. Ventura, 2022, The journal of physical chemistry. B.

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

A. Amadei, A. di Nola, M. D’Abramo, 2005, Journal of the American Chemical Society.

Structural analysis of water networks

Laura Zanetti Polzi, M. Benzi, I. Daidone, 2022, J. Complex Networks.

Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation

Caitlin M. Davis, M. Gruebele, A. Amadei, 2017, FEBS letters.

On the structural affinity of macromolecules with different biological properties: molecular dynamics simulations of a series of TEM-1 mutants.

I. Daidone, M. Aschi, G. Amicosante, 2013, Biochemical and biophysical research communications.

Evidence of a Thermodynamic Ramp for Hole Hopping to Protect a Redox Enzyme from Oxidative Damage.

I. Daidone, S. Corni, L. Zanetti‐Polzi, 2019, The journal of physical chemistry letters.

Allosteric control of naphthalene diimide encapsulation and electron transfer in porphyrin containers: photophysical studies and molecular dynamics simulation.

I. Daidone, B. Ventura, S. Durot, 2020, Chemistry.

Interpretation of Experimental Soret Bands of Porphyrins in Flexible Covalent Cages and in Their Related Ag(I) Fixed Complexes

A. Amadei, I. Daidone, B. Ventura, 2019, The Journal of Physical Chemistry C.

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

Laura Zanetti Polzi, A. Amadei, I. Daidone, 2012, The journal of physical chemistry. B.

Toward a Realistic Modeling of the Photophysics of Molecular Building Blocks for Energy Harvesting: The Charge-Transfer State in 4,7-Dithien-2-yl-2,1,3-benzothiadiazole As a Case Study

A. Amadei, I. Daidone, Andrea Alessi, 2013 .

Conformational study of bovine lactoferricin in membrane-micking conditions by molecular dynamics simulation and circular dichroism

A. di Nola, I. Daidone, A. Oratore, 2011, BioMetals.

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

A. Amadei, A. di Nola, I. Daidone, 2010, Current opinion in structural biology.

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

V. Barone, A. Amadei, I. Daidone, 2020, Physical chemistry chemical physics : PCCP.

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

A. Amadei, I. Daidone, M. Aschi, 2011, Journal of the American Chemical Society.

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

A. Amadei, I. Daidone, M. Aschi, 2013, The journal of physical chemistry. B.

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

Caitlin M. Davis, M. Gruebele, A. Amadei, 2018, Chemical science.

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

Jeremy C. Smith, A. Amadei, I. Daidone, 2015, The journal of physical chemistry. B.

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

Vincenzo Barone, Giordano Mancini, Andrea Amadei, 2018, J. Comput. Chem..

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

G. D'Inzeo, M. Liberti, F. Apollonio, 2013, Theoretical Chemistry Accounts.

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

V. Barone, A. Amadei, M. D’Abramo, 2018, Physical chemistry chemical physics : PCCP.

Theoretical modeling of the absorption spectrum of aqueous riboflavin

A. Amadei, I. Daidone, M. Aschi, 2017 .

Essential dynamics: foundation and applications

Andrea Amadei, Isabella Daidone, A. Amadei, 2012 .

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

Callum J. Dickson, C. Chipot, J. Gumbart, 2020, Chemical science.

High Water Density at Non-Ice-Binding Surfaces Contributes to the Hyperactivity of Antifreeze Proteins

V. Barone, I. Daidone, Akash Deep Biswas, 2021, The journal of physical chemistry letters.

The Hydration Shell of Antifreeze Proteins:Unveiling the Role of Non-Ice-Binding Surfaces.

V. Barone, I. Daidone, Akash Deep Biswas, 2019, The journal of physical chemistry. B.

High density water clusters observed at high concentrations of the macromolecular crowder PEG400

Sara Del Galdo, M. Chiarini, I. Daidone, 2022, Journal of Molecular Liquids.

Molecular origin of Gerstmann-Sträussler-Scheinker syndrome: insight from computer simulation of an amyloidogenic prion peptide.

Isabella Daidone, Jeremy C. Smith, Jeremy C Smith, 2011, Biophysical journal.

β‐Hairpin conformation of fibrillogenic peptides: Structure and α‐β transition mechanism revealed by molecular dynamics simulations

Guido Tiana, Isabella Daidone, Giorgio Colombo, 2004 .

A general theoretical model for electron transfer reactions in complex systems.

A. Amadei, I. Daidone, M. Aschi, 2012, Physical chemistry chemical physics : PCCP.

Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c.

Andrea Amadei, Alfredo Di Nola, Isabella Daidone, 2003, Biophysical journal.

Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding–unbinding reaction in Myoglobin

A. Amadei, M. D’Abramo, I. Daidone, 2007 .

Instantaneous normal modes and the protein glass transition.

Jeremy C. Smith, R. Schulz, I. Daidone, 2009, Biophysical journal.

On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study.

A. Amadei, I. Daidone, M. Aschi, 2018, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding

Andrea Amadei, Isabella Daidone, Jeremy C. Smith, 2007, Proceedings of the National Academy of Sciences.

Thermodynamic and kinetic characterization of a β‐hairpin peptide in solution: An extended phase space sampling by molecular dynamics simulations in explicit water

A. Amadei, A. di Nola, I. Daidone, 2005, Proteins.

A molecular dynamics study of acylphosphatase in aggregation‐promoting conditions: The influence of trifluoroethanol/water solvent

A. di Nola, I. Daidone, D. Flöck, 2004, Biopolymers.

Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling.

Isabella Daidone, Steven Hayward, Danilo Roccatano, 2004, Journal of molecular biology.

Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study.

M. Ceruso, I. Daidone, Cecilia Bossa, 2003, Biophysical journal.

Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design

Jeremy C. Smith, C. Chipot, J. Gumbart, 2021, The journal of physical chemistry letters.

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

F. Zaccanti, A. Amadei, I. Daidone, 2014, The journal of physical chemistry letters.

Alteration of water structure by peptide clusters revealed by neutron scattering in the small-angle region (below 1 Å(-1)).

Jeremy C. Smith, I. Daidone, C. Iacobucci, 2012, Biophysical journal.

A Fully Atomistic Multiscale Approach for pKa Prediction.

A. Amadei, I. Daidone, L. Zanetti‐Polzi, 2020, The journal of physical chemistry. B.

Structure and solvation properties of aqueous sulfobetaine micelles in the presence of organic spin probes: a Molecular Dynamics simulation study

M. Chiarini, I. Daidone, G. Cerichelli, 2013, Structural Chemistry.

Low- and high-density forms of liquid water revealed by a new medium-range order descriptor

M. Benzi, I. Daidone, Chiara Faccio, 2022, Journal of Molecular Liquids.

Alternative Electron-Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Excited States in Riboflavin Binding Protein.

A. Amadei, I. Daidone, M. Aschi, 2017, The journal of physical chemistry letters.

Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor

Arnold N. Tharrington, Jerry M. Parks, Russell B. Davidson, 2022, ACS pharmacology & translational science.

Segregation on the nanoscale coupled to liquid water polyamorphism in supercooled aqueous ionic-liquid solution.

A. Amadei, I. Daidone, L. Zanetti‐Polzi, 2021, The Journal of chemical physics.

Modeling quantum vibrational excitations in condensed-phase molecular systems

A. Amadei, I. Daidone, M. Aschi, 2011 .

On the origin of IR spectral changes upon protein folding

A. Amadei, I. Daidone, M. Aschi, 2010 .

Surface packing determines the redox potential shift of cytochrome c adsorbed on gold.

Isabella Daidone, Stefano Corni, I. Daidone, 2014, Journal of the American Chemical Society.

Length-scale dependence of protein hydration-shell density.

V. Barone, A. Amadei, I. Daidone, 2020, Physical chemistry chemical physics : PCCP.

Tuning proton transfer thermodynamics in SARS-Cov-2 main protease: implications for catalysis and inhibitor design

Jeremy C. Smith, C. Chipot, J. Gumbart, 2020, ChemRxiv : the preprint server for chemistry.

Cooperative protein-solvent tuning of proton transfer energetics: carbonic anhydrase as a case study.

I. Daidone, M. Aschi, L. Zanetti‐Polzi, 2020, Physical chemistry chemical physics : PCCP.

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

Jeremy C. Smith, Isabella Daidone, Markus Sauer, 2010, PLoS Comput. Biol..

Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations

Jeremy C. Smith, Isabella Daidone, Lipi Thukral, 2011, PLoS Comput. Biol..

Mechanism and Dynamics of Photodecarboxylation Catalyzed by Lactate Monooxygenase.

G. Scholes, I. Daidone, Daniel G. Oblinsky, 2023, Journal of the American Chemical Society.

Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico model.

V. Barone, A. Amadei, I. Daidone, 2016, Physical chemistry chemical physics : PCCP.

Structural and dynamical properties of KTS-disintegrins: A comparison between Obtustatin and Lebestatin.

I. Daidone, R. Petruzzelli, A. Bozzi, 2013, Biopolymers.

Aggregation of small peptides studied by molecular dynamics simulations

A. Amadei, I. Daidone, G. Rossetti, 2006, Proteins.

Tip-Enhanced Infrared Difference-Nanospectroscopy of the Proton Pump Activity of Bacteriorhodopsin in Single Purple Membrane Patches

P. Hegemann, P. Biagioni, I. Daidone, 2019, Nano letters.

Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteins.

A. Amadei, I. Daidone, S. Corni, 2016, Physical chemistry chemical physics : PCCP.

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

A. Amadei, I. Daidone, C. Bortolotti, 2015, Organic & biomolecular chemistry.

Unambiguous Assignment of Reduction Potentials in Diheme Cytochromes.

A. Amadei, I. Daidone, C. Bortolotti, 2014, The journal of physical chemistry. B.

Evidence for a high pK a of an aspartic acid residue in the active site of CALB by a fully atomistic multiscale approach

I. Daidone, N. Spreti, Matteo Capone, 2022, Journal of biomolecular structure & dynamics.

Subdiffusion in peptides originates from the fractal-like structure of configuration space.

Isabella Daidone, Jeremy C. Smith, Jeremy C Smith, 2008, Physical review letters.

Difference mid-IR nanospectroscopy on individual patches of purple membranes: the proton pump activity of bacteriorhodopsin at the nanoscale

P. Hegemann, P. Biagioni, I. Daidone, 2019, 2019 44th International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz).

Computational evidence support the hypothesis of neuroglobin also acting as an electron transfer species

A. Ranieri, I. Daidone, C. Bortolotti, 2017, JBIC Journal of Biological Inorganic Chemistry.

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

A. Amadei, A. di Nola, G. Colombo, 2005, Proteins.

Theoretical-computational characterization of the temperature-dependent folding thermodynamics of a β-hairpin peptide

A. Amadei, I. Daidone, Lipi Thukral, 2016 .

Protein Folding Pathways Revealed by Essential Dynamics Sampling.

A. Amadei, A. di Nola, I. Daidone, 2008, Journal of chemical theory and computation.

A statistical mechanical model of supercooled water based on minimal clusters of correlated molecules.

A. Amadei, I. Daidone, L. Zanetti‐Polzi, 2023, The Journal of chemical physics.

Thermodynamic Evolution of a Metamorphic Protein: A Theoretical-Computational Study of Human Lymphotactin

A. Amadei, I. Daidone, C. Iacobucci, 2023, The Protein Journal.

Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c.

A. Amadei, I. Daidone, D. Roccatano, 2003, Biophysical journal.

Instantaneous normal modes and the protein glass transition.

Jeremy C. Smith, R. Schulz, I. Daidone, 2009, Biophysical journal.

Enhanced Connectivity and Mobility in Liquid Water: Implications for the High Density Liquid Structure and its Onset

I. Daidone, Chiara Faccio, L. Zanetti‐Polzi, 2023, Journal of Molecular Liquids.