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Isabella Daidone
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Supercomputer-based ensemble docking drug discovery pipeline with application to COVID-19
A Acharya, R Agarwal, MB Baker, J Baudry, D Bhowmik, S Boehm, ...
Journal of chemical information and modeling 60 (12), 5832-5852, 2020
1552020
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments
F Noé, S Doose, I Daidone, M Löllmann, M Sauer, JD Chodera, JC Smith
Proceedings of the National Academy of Sciences 108 (12), 4822, 2011
1422011
Essential dynamics: foundation and applications
I Daidone, A Amadei
Wiley Interdisciplinary Reviews: Computational Molecular Science 2 (5), 762-770, 2012
1222012
β‐Hairpin conformation of fibrillogenic peptides: Structure and α‐β transition mechanism revealed by molecular dynamics simulations
I Daidone, F Simona, D Roccatano, RA Broglia, G Tiana, G Colombo, ...
Proteins: Structure, Function, and Bioinformatics 57 (1), 198-204, 2004
1122004
Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities
C Bossa, A Amadei, I Daidone, M Anselmi, B Vallone, M Brunori, ...
Biophysical Journal 89 (1), 465-474, 2005
1102005
Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c
I Daidone, A Amadei, D Roccatano, A Di Nola
Biophysical journal 85 (5), 2865-2871, 2003
872003
Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding
I Daidone, MB Ulmschneider, A Di Nola, A Amadei, JC Smith
Proceedings of the National Academy of Sciences 104 (39), 15230-15235, 2007
822007
Subdiffusion in peptides originates from the fractal-like structure of configuration space
T Neusius, I Daidone, IM Sokolov, JC Smith
Physical review letters 100 (18), 188103, 2008
812008
The Reversible Opening of Water Channels in Cytochrome c Modulates the Heme Iron Reduction Potential
CA Bortolotti, A Amadei, M Aschi, M Borsari, S Corni, M Sola, I Daidone
Journal of the American Chemical Society 134 (33), 13670-13678, 2012
792012
Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains
I Daidone, H Neuweiler, S Doose, M Sauer, JC Smith
PLoS computational biology 6 (1), e1000645, 2010
632010
Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease
A Pavlova, DL Lynch, I Daidone, L Zanetti-Polzi, MD Smith, C Chipot, ...
Chemical science 12 (4), 1513-1527, 2021
592021
Thermodynamic and kinetic characterization of a β‐hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water
I Daidone, A Amadei, A Di Nola
Proteins: Structure, Function, and Bioinformatics 59 (3), 510-518, 2005
572005
Molecular dynamics simulation of the aggregation of the core‐recognition motif of the islet amyloid polypeptide in explicit water
G Colombo, I Daidone, E Gazit, A Amadei, A Di Nola
Proteins: Structure, Function, and Bioinformatics 59 (3), 519-527, 2005
562005
Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory
L Zanetti-Polzi, S Del Galdo, I Daidone, M D'Abramo, V Barone, M Aschi, ...
Physical Chemistry Chemical Physics 20 (37), 24369-24378, 2018
522018
Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study
D Roccatano, I Daidone, MA Ceruso, C Bossa, A Di Nola
Biophysical journal 84 (3), 1876-1883, 2003
522003
Theoretical characterization of α-helix and β-hairpin folding kinetics
I Daidone, M D'Abramo, A Di Nola, A Amadei
Journal of the American Chemical Society 127 (42), 14825-14832, 2005
482005
Charge-based interactions between peptides observed as the dominant force for association in aqueous solution
SE McLain, AK Soper, I Daidone, JC Smith, A Watts
Angew. Chem., Int. Ed 47 (47), 9059-9062, 2008
472008
Tip-enhanced infrared difference-nanospectroscopy of the proton pump activity of bacteriorhodopsin in single purple membrane patches
V Giliberti, R Polito, E Ritter, M Broser, P Hegemann, L Puskar, U Schade, ...
Nano letters 19 (5), 3104-3114, 2019
462019
Surface packing determines the redox potential shift of cytochrome c adsorbed on gold
L Zanetti-Polzi, I Daidone, CA Bortolotti, S Corni
Journal of the American Chemical Society 136 (37), 12929-12937, 2014
462014
Theoretical modeling of the absorption spectrum of aqueous riboflavin
L Zanetti-Polzi, M Aschi, I Daidone, A Amadei
Chemical Physics Letters 669, 119-124, 2017
432017
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