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Essential dynamics: foundation and applications

Wiley interdisciplinary reviews. Computational molecular science, 2012-09, Vol.2 (5), p.762-770

2012

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Alternative Fast and Slow Primary Charge‐Separation Pathways in Photosystem II

Angewandte Chemie International Edition, 2023-04, Vol.62 (16), p.e202216276-n/a

International ed. in English, 2023

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Surface Packing Determines the Redox Potential Shift of Cytochrome c Adsorbed on Gold

Journal of the American Chemical Society, 2014-09, Vol.136 (37), p.12929-12937

2014

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

Proceedings of the National Academy of Sciences - PNAS, 2011-03, Vol.108 (12), p.4822-4827

2011

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Molecular Dynamics Simulation of Sperm Whale Myoglobin: Effects of Mutations and Trapped CO on the Structure and Dynamics of Cavities

Biophysical journal, 2005-07, Vol.89 (1), p.465-474

2005

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Fully Atomistic Multiscale Approach for p K a Prediction

The journal of physical chemistry. B, 2020-06, Vol.124 (23), p.4712-4722

2020

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A combined experimental and computational approach for the rationalization of the catalytic activity of lipase B from Candida antarctica in water–organic solvent mixtures

Journal of chemical technology and biotechnology (1986), 2023-10, Vol.98 (10), p.2429-2436

2023

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

Proteins, structure, function, and bioinformatics, 2005-05, Vol.59 (3), p.519-527

2005

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Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c

Biophysical journal, 2003-11, Vol.85 (5), p.2865-2871

2003

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Il Piano Programma per Palermo e i PRG per Urbino

Agathón (Online), 2017-06, Vol.1 (online)

Isabella Daidone

2017

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Excitation landscape of the CP43 photosynthetic antenna complex from multiscale simulations

Chemical science (Cambridge), 2024-05, Vol.15 (19), p.7269-7284

2024

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Unique Electron Donor–Acceptor Complex Conformation Ensures Both the Efficiency and Enantioselectivity of Photoinduced Radical Cyclization in a Non-natural Photoenzyme

ACS catalysis, 2024-10, p.16488-16496

2024

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

The journal of physical chemistry. B, 2019-08, Vol.123 (30), p.6474-6480

2019

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Applying Computational Spectroscopy Methods to Raman Spectra of Dicationic, Imidazolium-Based, Ionic Liquids

The journal of physical chemistry. B, 2024-10

2024

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Mechanisms in the Synthesis of S-Alcohols with 1,4-NADH Biomimetic Co-factor N-Benzyl-1,4-dihydronicotinamide using Horse Liver Alcohol Dehydrogenase: A Hybrid Computational Study

Chembiochem : a European journal of chemical biology, 2024-09, p.e202400727

2024

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Structural analysis of water networks

Journal of complex networks, 2022-12, Vol.11 (1)

2022

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Evidence of a Distinctive Enantioselective Binding Mode for the Photoinduced Radical Cyclization of α-Chloroamides in Ene-Reductases

ACS catalysis, 2023-12, Vol.13 (23), p.15310-15321

2023

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

Journal of physical chemistry. C, 2019-05, Vol.123 (20), p.13094-13103

2019

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Allosteric Control of Naphthalene Diimide Encapsulation and Electron Transfer in Porphyrin Containers: Photophysical Studies and Molecular Dynamics Simulation

Chemistry : a European journal, 2020-12, Vol.26 (72), p.17514-17524

2020

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

RSC advances, 2013-01, Vol.3 (42), p.19657-19665

2013

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Fully Atomistic Multiscale Approach for pKa Prediction

The journal of physical chemistry. B, 2020-06, Vol.124 (23), p.4712-4722

2020

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Intermolecular Photoinduced Electron Transfer in Biosystems: Impact of Conformational Transitions and Multiple Channels on Kinetics

ChemPhotoChem, 2024-07, Vol.8 (7), p.n/a

2024

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Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteinsElectronic supplementary information (ESI) available: Additional analysis on the two azurin mutants Mut1 and Mut2. See DOI: 10.1039/c6cp03394f

2016-07

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

Journal of computational chemistry, 2018-08, Vol.39 (22), p.1747-1756

2018

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

The journal of physical chemistry. B, 2022-05, Vol.126 (18), p.3450-3459

2022

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ThemaMolecular Dynamics Simulation

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Essential dynamics: foundation and applications

Alternative Fast and Slow Primary Charge‐Separation Pathways in Photosystem II

Surface Packing Determines the Redox Potential Shift of Cytochrome c Adsorbed on Gold

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

Molecular Dynamics Simulation of Sperm Whale Myoglobin: Effects of Mutations and Trapped CO on the Structure and Dynamics of Cavities

Fully Atomistic Multiscale Approach for p K a Prediction

A combined experimental and computational approach for the rationalization of the catalytic activity of lipase B from Candida antarctica in water–organic solvent mixtures

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

Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c

Il Piano Programma per Palermo e i PRG per Urbino

Excitation landscape of the CP43 photosynthetic antenna complex from multiscale simulations

Unique Electron Donor–Acceptor Complex Conformation Ensures Both the Efficiency and Enantioselectivity of Photoinduced Radical Cyclization in a Non-natural Photoenzyme

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

Applying Computational Spectroscopy Methods to Raman Spectra of Dicationic, Imidazolium-Based, Ionic Liquids

Mechanisms in the Synthesis of S-Alcohols with 1,4-NADH Biomimetic Co-factor N-Benzyl-1,4-dihydronicotinamide using Horse Liver Alcohol Dehydrogenase: A Hybrid Computational Study

Structural analysis of water networks

Evidence of a Distinctive Enantioselective Binding Mode for the Photoinduced Radical Cyclization of α-Chloroamides in Ene-Reductases

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

Allosteric Control of Naphthalene Diimide Encapsulation and Electron Transfer in Porphyrin Containers: Photophysical Studies and Molecular Dynamics Simulation

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

Fully Atomistic Multiscale Approach for pKa Prediction

Intermolecular Photoinduced Electron Transfer in Biosystems: Impact of Conformational Transitions and Multiple Channels on Kinetics

Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteinsElectronic supplementary information (ESI) available: Additional analysis on the two azurin mutants Mut1 and Mut2. See DOI: 10.1039/c6cp03394f

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

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

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