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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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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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Investigating the Accessibility of the Closed Domain Conformation of Citrate Synthase using Essential Dynamics Sampling

Journal of molecular biology, 2004-06, Vol.339 (3), p.515-525

2004

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

The Protein Journal, 2023-06, Vol.42 (3), p.219-228

2023

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

Journal of biomolecular structure & dynamics, 2023-07, Vol.41 (11), p.4949-4956

2023

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Structural analysis of water networks

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

2022

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

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy, 2018-03, Vol.192, p.451-457

2018

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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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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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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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Unambiguous Assignment of Reduction Potentials in Diheme Cytochromes

The journal of physical chemistry. B, 2014-07, Vol.118 (27), p.7554-7560

2014

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A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopyElectronic supplementary information (ESI) available: Temperature-dependent circular dichroism and FTIR, SVD analysis of the FTIR data, global fitting of thermal melts, Arrhenius plots of observed kinetics, expanded computational methods, the computational distribution of IR intensities, and complete tables of relaxation kinetics of 1619 cm−1, 1634 cm−1, 1661 cm−1 and 1680 cm−1. See DOI: 10.1039

2018-12

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A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy† †Electronic supplementary information (ESI) available: Temperature-dependent circular dichroism and FTIR, SVD analysis of the FTIR data, global fitting of thermal melts, Arrhenius plots of observed kinetics, expanded computational methods, the computational distribution of IR intensities, and complete tables of relaxation kinetics of 1619 cm–1, 1634 cm–1, 1661 cm–1 and 1680 cm–1. See DOI: 10.1

Chemical science (Cambridge), 2018-10, Vol.9 (48), p.9002-9011

2018

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

Journal of biomolecular structure & dynamics, 2023-07, Vol.41 (11), p.4949-4956

2023

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

Angewandte Chemie, 2023-04, Vol.135 (16), p.n/a

2023

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Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico modelElectronic supplementary information (ESI) available. See DOI: 10.1039/c6cp06167b

2016-10

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Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solutionElectronic supplementary information (ESI) available. See DOI: 10.1039/c4cp02422b

2014-09

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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

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

Investigating the Accessibility of the Closed Domain Conformation of Citrate Synthase using Essential Dynamics Sampling

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

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

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

Structural analysis of water networks

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

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

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

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

Unambiguous Assignment of Reduction Potentials in Diheme Cytochromes

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

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

Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico modelElectronic supplementary information (ESI) available. See DOI: 10.1039/c6cp06167b

Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solutionElectronic supplementary information (ESI) available. See DOI: 10.1039/c4cp02422b

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