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

ACS pharmacology & translational science, 2022-04, Vol.5 (4), p.255-265

2022

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

Proteins, structure, function, and bioinformatics, 2005-05, Vol.59 (3), p.510-518

2005

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

Proteins, structure, function, and bioinformatics, 2004-10, Vol.57 (1), p.198-204

2004

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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

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

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

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

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

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

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

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

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