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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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Il Piano Programma per Palermo e i PRG per Urbino

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

Isabella Daidone

2017

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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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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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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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A few key residues determine the high redox potential shift in azurin mutantsElectronic supplementary information (ESI) available: Additional details of the quantum centre and additional analyses of the mutants' properties. See DOI: 10.1039/c5ob01819f

2015-11

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Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations: e1002137

PLoS computational biology, 2011-09, Vol.7 (9)

2011

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

Journal of chemical information and modeling, 2020-12, Vol.60 (12)

2020

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

Journal of chemical information and modeling, 2020-12, Vol.60 (12)

2020

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Common Folding Mechanism of a Peptide Revealed by Multiple MD Simulations

Biophysical journal, 2010-01, Vol.98 (3), p.199a-200a

2010

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Molecular Origin of Gerstmann-Straeussler-Scheinker Syndrome: Insight from Computer Simulation of an Amyloidogenic Prion Peptide

Biophysical journal, 2011-06, Vol.100 (12), p.3000-3007

2011

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Mechanism of DNA Recognition by EcoRV

Biophysical journal, 2010-01, Vol.98 (3), p.444a-444a

2010

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Instantaneous Normal Modes and the Protein Glass Transition

Biophysical journal, 2009-01, Vol.96 (2)

2009

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Subdiffusion in Peptides Originates from the Fractal-Like Structure of Configuration Space

Physical review letters, 2008-05, Vol.100 (18)

2008

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Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains: e1000645

PLoS computational biology, 2010-01, Vol.6 (1)

2010

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Dehydration-Driven Solvent Exposure of Hydrophobic Surfaces as a Driving Force in Peptide Folding

Proceedings of the National Academy of Sciences - PNAS, 2007-09, Vol.104 (39)

2007

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Charge‐Based Interactions between Peptides Observed as the Dominant Force for Association in Aqueous Solution

Angewandte Chemie, 2008-11, Vol.120 (47), p.9199-9202

2008

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Charge‐Based Interactions between Peptides Observed as the Dominant Force for Association in Aqueous Solution

Angewandte Chemie, 2008-11, Vol.120 (47), p.9199-9202

2008

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Charge-based interactions between peptides observed as the dominant force for association in aqueous solution

Angewandte Chemie (International ed.), 2008-10, Vol.47 (47)

2008

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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

Il Piano Programma per Palermo e i PRG per Urbino

Fully Atomistic Multiscale Approach for pKa Prediction

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

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

A few key residues determine the high redox potential shift in azurin mutantsElectronic supplementary information (ESI) available: Additional details of the quantum centre and additional analyses of the mutants' properties. See DOI: 10.1039/c5ob01819f

Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations: e1002137

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

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

Common Folding Mechanism of a Peptide Revealed by Multiple MD Simulations

Molecular Origin of Gerstmann-Straeussler-Scheinker Syndrome: Insight from Computer Simulation of an Amyloidogenic Prion Peptide

Mechanism of DNA Recognition by EcoRV

Instantaneous Normal Modes and the Protein Glass Transition

Subdiffusion in Peptides Originates from the Fractal-Like Structure of Configuration Space

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains: e1000645

Dehydration-Driven Solvent Exposure of Hydrophobic Surfaces as a Driving Force in Peptide Folding

Charge‐Based Interactions between Peptides Observed as the Dominant Force for Association in Aqueous Solution

Charge‐Based Interactions between Peptides Observed as the Dominant Force for Association in Aqueous Solution

Charge-based interactions between peptides observed as the dominant force for association in aqueous solution

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