| Year |
Citation |
Score |
| 2023 |
Zanetti-Polzi L, Daidone I, Iacobucci C, Amadei A. Thermodynamic Evolution of a Metamorphic Protein: A Theoretical-Computational Study of Human Lymphotactin. The Protein Journal. 42: 219-228. PMID 37233895 DOI: 10.1007/s10930-023-10123-7 |
0.345 |
|
| 2021 |
Pinto SMV, Tasinato N, Barone V, Zanetti-Polzi L, Daidone I. A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures. The Journal of Chemical Physics. 154: 084105. PMID 33639764 DOI: 10.1063/5.0038913 |
0.341 |
|
| 2020 |
Zanetti-Polzi L, Aschi M, Daidone I. Cooperative protein-solvent tuning of proton transfer energetics: carbonic anhydrase as a case study. Physical Chemistry Chemical Physics : Pccp. PMID 32857091 DOI: 10.1039/D0Cp03652H |
0.333 |
|
| 2020 |
Ventura B, Zanetti-Polzi L, Djemili R, Durot S, Heitz V, Daidone I. Allosteric control of naphthalene diimide encapsulation and electron transfer in porphyrin containers: photophysical studies and molecular dynamics simulation. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 32845572 DOI: 10.1002/Chem.202003151 |
0.409 |
|
| 2020 |
Zanetti-Polzi L, Daidone I, Amadei A. A Fully Atomistic Multiscale Approach for Prediction. The Journal of Physical Chemistry. B. PMID 32427481 DOI: 10.1021/Acs.Jpcb.0C01752 |
0.357 |
|
| 2020 |
Biswas AD, Barone V, Amadei A, Daidone I. Length-scale dependence of protein hydration-shell density. Physical Chemistry Chemical Physics : Pccp. PMID 32211621 DOI: 10.1039/C9Cp06214A |
0.338 |
|
| 2020 |
Vieira Pinto SM, Tasinato N, Barone V, Amadei A, Zanetti-Polzi L, Daidone I. Modeling amino-acid side chain infrared spectra: the case of carboxylic residues. Physical Chemistry Chemical Physics : Pccp. PMID 31957772 DOI: 10.1039/C9Cp04774C |
0.401 |
|
| 2019 |
Giliberti V, Polito R, Ritter E, Broser M, Hegemann P, Puskar L, Schade U, Zanetti-Polzi L, Daidone I, Corni S, Rusconi F, Biagioni P, Baldassarre L, Ortolani M. Tip-enhanced Infrared Difference-Nanospectroscopy of the Proton Pump Activity of Bacteriorhodopsin in Single Purple Membrane Patches. Nano Letters. PMID 30950626 DOI: 10.1021/Acs.Nanolett.9B00512 |
0.334 |
|
| 2019 |
Zanetti-Polzi L, Daidone I, Corni S. Evidence of a Thermodynamic Ramp for Hole Hopping to Protect a Redox Enzyme from Oxidative Damage. The Journal of Physical Chemistry Letters. 1450-1456. PMID 30855973 DOI: 10.1021/Acs.Jpclett.9B00403 |
0.352 |
|
| 2018 |
Davis CM, Zanetti-Polzi L, Gruebele M, Amadei A, Dyer RB, Daidone I. A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy. Chemical Science. 9: 9002-9011. PMID 30647892 DOI: 10.1039/C8Sc03786H |
0.509 |
|
| 2018 |
Zanetti-Polzi L, Del Galdo S, Daidone I, D'Abramo M, Barone V, Aschi M, Amadei A. Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory. Physical Chemistry Chemical Physics : Pccp. PMID 30215645 DOI: 10.1039/C8Cp04190C |
0.361 |
|
| 2018 |
Del Galdo S, Mancini G, Daidone I, Zanetti Polzi L, Amadei A, Barone V. Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties. Journal of Computational Chemistry. PMID 29756218 DOI: 10.1002/Jcc.25351 |
0.431 |
|
| 2017 |
Daidone I, Amadei A, Aschi M, Zanetti-Polzi L. On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 192: 451-457. PMID 29212059 DOI: 10.1016/J.Saa.2017.11.031 |
0.353 |
|
| 2017 |
Zanetti-Polzi L, Davis CM, Gruebele M, Dyer RB, Amadei A, Daidone I. Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. Febs Letters. PMID 28881468 DOI: 10.1002/1873-3468.12836 |
0.413 |
|
| 2017 |
Zanetti-Polzi L, Aschi M, Amadei A, Daidone I. Alternative Electron Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Excited States in Riboflavin Binding Protein. The Journal of Physical Chemistry Letters. PMID 28665138 DOI: 10.1021/Acs.Jpclett.7B01575 |
0.355 |
|
| 2017 |
Paltrinieri L, Di Rocco G, Battistuzzi G, Borsari M, Sola M, Ranieri A, Zanetti-Polzi L, Daidone I, Bortolotti CA. Computational evidence support the hypothesis of neuroglobin also acting as an electron transfer species. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. PMID 28378164 DOI: 10.1007/S00775-017-1455-2 |
0.336 |
|
| 2017 |
Zanetti-Polzi L, Aschi M, Daidone I, Amadei A. Theoretical modeling of the absorption spectrum of aqueous riboflavin Chemical Physics Letters. 669: 119-124. DOI: 10.1016/J.Cplett.2016.12.022 |
0.35 |
|
| 2016 |
Aschi M, Barone V, Carlotti B, Daidone I, Elisei F, Amadei A. Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico model. Physical Chemistry Chemical Physics : Pccp. PMID 27725986 DOI: 10.1039/C6Cp06167B |
0.431 |
|
| 2016 |
Guzzo T, Mandaliti W, Nepravishta R, Aramini A, Bodo E, Daidone I, Allegretti M, Topai A, Paci M. Conformational Change in the Mechanism of Inclusion of Ketoprofen in β-Cyclodextrin: NMR Spectroscopy, Ab Initio Calculations, Molecular Dynamics Simulations, and Photoreactivity. The Journal of Physical Chemistry. B. 120: 10668-10678. PMID 27689813 DOI: 10.1021/Acs.Jpcb.6B07913 |
0.362 |
|
| 2016 |
Zanetti-Polzi L, Corni S, Daidone I, Amadei A. Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteins. Physical Chemistry Chemical Physics : Pccp. 18: 18450-9. PMID 27339768 DOI: 10.1039/C6Cp03394F |
0.408 |
|
| 2016 |
Daidone I, Zanetti-Polzi L, Thukral L, Alekozai EM, Amadei A. Theoretical-computational characterization of the temperature-dependent folding thermodynamics of a β-hairpin peptide Chemical Physics Letters. 659: 247-251. DOI: 10.1016/J.Cplett.2016.07.041 |
0.436 |
|
| 2015 |
Zanetti-Polzi L, Bortolotti CA, Daidone I, Aschi M, Amadei A, Corni S. A few key residues determine the high redox potential shift in azurin mutants. Organic & Biomolecular Chemistry. 13: 11003-13. PMID 26381463 DOI: 10.1039/C5Ob01819F |
0.373 |
|
| 2015 |
Thukral L, Schwarze S, Daidone I, Neuweiler H. β-Structure within the Denatured State of the Helical Protein Domain BBL. Journal of Molecular Biology. 427: 3166-76. PMID 26281710 DOI: 10.1016/J.Jmb.2015.08.007 |
0.429 |
|
| 2015 |
Daidone I, Thukral L, Smith JC, Amadei A. Monitoring the folding kinetics of a β-hairpin by time-resolved IR spectroscopy in silico. The Journal of Physical Chemistry. B. 119: 4849-56. PMID 25777154 DOI: 10.1021/Acs.Jpcb.5B01477 |
0.48 |
|
| 2014 |
Daidone I, Amadei A, Zaccanti F, Borsari M, Bortolotti CA. How the Reorganization Free Energy Affects the Reduction Potential of Structurally Homologous Cytochromes. The Journal of Physical Chemistry Letters. 5: 1534-40. PMID 26270092 DOI: 10.1021/Jz5005208 |
0.336 |
|
| 2014 |
Zanetti-Polzi L, Daidone I, Bortolotti CA, Corni S. Surface packing determines the redox potential shift of cytochrome c adsorbed on gold. Journal of the American Chemical Society. 136: 12929-37. PMID 25184441 DOI: 10.1021/Ja505251A |
0.36 |
|
| 2014 |
Piacente G, Amadei A, D'Abramo M, Daidone I, Aschi M. Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solution. Physical Chemistry Chemical Physics : Pccp. 16: 20624-38. PMID 25157909 DOI: 10.1039/C4Cp02422B |
0.372 |
|
| 2014 |
Daidone I, Paltrinieri L, Amadei A, Battistuzzi G, Sola M, Borsari M, Bortolotti CA. Unambiguous Assignment of Reduction Potentials in Diheme Cytochromes. The Journal of Physical Chemistry. B. PMID 24950346 DOI: 10.1021/Jp506017A |
0.345 |
|
| 2013 |
Zanetti-Polzi L, Aschi M, Amadei A, Daidone I. Simulation of the amide I infrared spectrum in photoinduced peptide folding/unfolding transitions. The Journal of Physical Chemistry. B. 117: 12383-90. PMID 24044356 DOI: 10.1021/Jp406708P |
0.452 |
|
| 2013 |
Giampaolo AD, Mazza F, Daidone I, Amicosante G, Perilli M, Aschi M. On the structural affinity of macromolecules with different biological properties: molecular dynamics simulations of a series of TEM-1 mutants. Biochemical and Biophysical Research Communications. 436: 666-71. PMID 23770365 DOI: 10.1016/J.Bbrc.2013.06.013 |
0.453 |
|
| 2013 |
Daidone I, Aschi M, Patamia M, Bozzi A, Petruzzelli R. Structural and dynamical properties of KTS-disintegrins: A comparison between Obtustatin and Lebestatin. Biopolymers. 99: 47-54. PMID 23097229 DOI: 10.1002/Bip.22138 |
0.34 |
|
| 2013 |
Amadei A, Daidone I, Bortolotti CA. A general statistical mechanical approach for modeling redox thermodynamics: the reaction and reorganization free energies Rsc Advances. 3: 19657. DOI: 10.1039/C3Ra42842G |
0.367 |
|
| 2013 |
D’Alessandro M, Amadei A, Daidone I, Po’ R, Alessi A, Aschi M. Toward a Realistic Modeling of the Photophysics of Molecular Building Blocks for Energy Harvesting: The Charge-Transfer State in 4,7-Dithien-2-yl-2,1,3-benzothiadiazole As a Case Study The Journal of Physical Chemistry C. 117: 13785-13797. DOI: 10.1021/Jp401173S |
0.348 |
|
| 2013 |
Giampaolo AD, Cerichelli G, Chiarini M, Daidone I, Aschi M. Structure and solvation properties of aqueous sulfobetaine micelles in the presence of organic spin probes: a Molecular Dynamics simulation study Structural Chemistry. 24: 945-953. DOI: 10.1007/S11224-013-0207-3 |
0.42 |
|
| 2013 |
Zanetti-Polzi L, Marracino P, Aschi M, Daidone I, Fontana A, Apollonio F, Liberti M, D’Inzeo G, Amadei A. Modeling triplet flavin-indole electron transfer and interradical dipolar interaction: a perturbative approach Theoretical Chemistry Accounts. 132. DOI: 10.1007/S00214-013-1393-1 |
0.352 |
|
| 2012 |
Daidone I, Iacobucci C, McLain SE, Smith JC. Alteration of water structure by peptide clusters revealed by neutron scattering in the small-angle region (below 1 Å(-1)). Biophysical Journal. 103: 1518-24. PMID 23062344 DOI: 10.1016/J.Bpj.2012.08.010 |
0.344 |
|
| 2012 |
Bortolotti CA, Amadei A, Aschi M, Borsari M, Corni S, Sola M, Daidone I. The reversible opening of water channels in cytochrome c modulates the heme iron reduction potential. Journal of the American Chemical Society. 134: 13670-8. PMID 22873369 DOI: 10.1021/Ja3030356 |
0.413 |
|
| 2012 |
Polzi LZ, Daidone I, Amadei A. A theoretical reappraisal of polylysine in the investigation of secondary structure sensitivity of infrared spectra. The Journal of Physical Chemistry. B. 116: 3353-60. PMID 22397736 DOI: 10.1021/Jp211063X |
0.365 |
|
| 2012 |
Amadei A, Daidone I, Aschi M. A general theoretical model for electron transfer reactions in complex systems. Physical Chemistry Chemical Physics : Pccp. 14: 1360-70. PMID 22158942 DOI: 10.1039/C1Cp22309G |
0.388 |
|
| 2012 |
Daidone I, Amadei A. Essential dynamics: foundation and applications Wiley Interdisciplinary Reviews: Computational Molecular Science. 2: 762-770. DOI: 10.1002/Wcms.1099 |
0.427 |
|
| 2011 |
Thukral L, Daidone I, Smith JC. Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations. Plos Computational Biology. 7: e1002137. PMID 21931542 DOI: 10.1371/Journal.Pcbi.1002137 |
0.484 |
|
| 2011 |
Zanetti Polzi L, Daidone I, Anselmi M, Carchini G, Di Nola A, Amadei A. Analysis of infrared spectra of β-hairpin peptides as derived from molecular dynamics simulations. The Journal of Physical Chemistry. B. 115: 11872-8. PMID 21895000 DOI: 10.1021/Jp202332Z |
0.442 |
|
| 2011 |
Zanetti Polzi L, Amadei A, Aschi M, Daidone I. New insight into the IR-spectra/structure relationship in amyloid fibrils: a theoretical study on a prion peptide. Journal of the American Chemical Society. 133: 11414-7. PMID 21692535 DOI: 10.1021/Ja2028662 |
0.442 |
|
| 2011 |
Daidone I, Di Nola A, Smith JC. Molecular origin of Gerstmann-Sträussler-Scheinker syndrome: insight from computer simulation of an amyloidogenic prion peptide. Biophysical Journal. 100: 3000-7. PMID 21689534 DOI: 10.1016/J.Bpj.2011.04.053 |
0.447 |
|
| 2011 |
Neusius T, Daidone I, Sokolov IM, Smith JC. Configurational subdiffusion of peptides: a network study. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 83: 021902. PMID 21405858 DOI: 10.1103/Physreve.83.021902 |
0.727 |
|
| 2011 |
Noé F, Doose S, Daidone I, Löllmann M, Sauer M, Chodera JD, Smith JC. Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proceedings of the National Academy of Sciences of the United States of America. 108: 4822-7. PMID 21368203 DOI: 10.1073/Pnas.1004646108 |
0.483 |
|
| 2011 |
Daidone I, Magliano A, Di Nola A, Mignogna G, Clarkson MM, Lizzi AR, Oratore A, Mazza F. Conformational study of bovine lactoferricin in membrane-micking conditions by molecular dynamics simulation and circular dichroism. Biometals : An International Journal On the Role of Metal Ions in Biology, Biochemistry, and Medicine. 24: 259-68. PMID 21088870 DOI: 10.1007/S10534-010-9390-5 |
0.42 |
|
| 2011 |
Amadei A, Daidone I, Zanetti-Polzi L, Aschi M. Modeling quantum vibrational excitations in condensed-phase molecular systems Theoretical Chemistry Accounts. 129: 31-43. DOI: 10.1007/S00214-010-0882-8 |
0.395 |
|
| 2010 |
Amadei A, Daidone I, Di Nola A, Aschi M. Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations. Current Opinion in Structural Biology. 20: 155-61. PMID 20116996 DOI: 10.1016/J.Sbi.2010.01.001 |
0.464 |
|
| 2010 |
Daidone I, Neuweiler H, Doose S, Sauer M, Smith JC. Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains. Plos Computational Biology. 6: e1000645. PMID 20098498 DOI: 10.1371/Journal.Pcbi.1000645 |
0.431 |
|
| 2010 |
Daidone I, Aschi M, Zanetti-Polzi L, Di Nola A, Amadei A. On the origin of IR spectral changes upon protein folding Chemical Physics Letters. 488: 213-218. DOI: 10.1016/J.Cplett.2010.02.020 |
0.376 |
|
| 2010 |
Thukral L, Smith JC, Daidone I. Common Folding Mechanism of a Peptide Revealed by Multiple MD Simulations Biophysical Journal. 98: 199a-200a. DOI: 10.1016/J.Bpj.2009.12.1065 |
0.492 |
|
| 2009 |
Thukral L, Smith JC, Daidone I. Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. Journal of the American Chemical Society. 131: 18147-52. PMID 19919102 DOI: 10.1021/Ja9064365 |
0.486 |
|
| 2009 |
Schulz R, Krishnan M, Daidone I, Smith JC. Instantaneous normal modes and the protein glass transition. Biophysical Journal. 96: 476-84. PMID 19167298 DOI: 10.1016/J.Bpj.2008.10.007 |
0.32 |
|
| 2008 |
Narzi D, Daidone I, Amadei A, Di Nola A. Protein Folding Pathways Revealed by Essential Dynamics Sampling. Journal of Chemical Theory and Computation. 4: 1940-8. PMID 26620336 DOI: 10.1021/Ct800157V |
0.44 |
|
| 2008 |
Noé F, Daidone I, Smith JC, di Nola A, Amadei A. Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation. The Journal of Physical Chemistry. B. 112: 11155-63. PMID 18698708 DOI: 10.1021/Jp801391T |
0.483 |
|
| 2008 |
Neusius T, Daidone I, Sokolov IM, Smith JC. Subdiffusion in peptides originates from the fractal-like structure of configuration space. Physical Review Letters. 100: 188103. PMID 18518418 DOI: 10.1103/Physrevlett.100.188103 |
0.724 |
|
| 2007 |
Daidone I, Ulmschneider MB, Di Nola A, Amadei A, Smith JC. Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proceedings of the National Academy of Sciences of the United States of America. 104: 15230-5. PMID 17881585 DOI: 10.1073/Pnas.0701401104 |
0.447 |
|
| 2007 |
Amadei A, D’Abramo M, Daidone I, D’Alessandro M, Nola AD, Aschi M. Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding–unbinding reaction in Myoglobin Theoretical Chemistry Accounts. 117: 637-647. DOI: 10.1007/S00214-006-0197-Y |
0.715 |
|
| 2006 |
Flöck D, Rossetti G, Daidone I, Amadei A, Di Nola A. Aggregation of small peptides studied by molecular dynamics simulations. Proteins. 65: 914-21. PMID 16981204 DOI: 10.1002/Prot.21168 |
0.422 |
|
| 2006 |
Aschi M, D'Abramo M, Ramondo F, Daidone I, D'Alessandro M, Di Nola A, Amadei A. Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde Journal of Physical Organic Chemistry. 19: 518-530. DOI: 10.1002/Poc.1051 |
0.416 |
|
| 2005 |
Daidone I, D'Abramo M, Di Nola A, Amadei A. Theoretical characterization of alpha-helix and beta-hairpin folding kinetics. Journal of the American Chemical Society. 127: 14825-32. PMID 16231936 DOI: 10.1021/Ja053383F |
0.405 |
|
| 2005 |
Bossa C, Amadei A, Daidone I, Anselmi M, Vallone B, Brunori M, Di Nola A. Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities. Biophysical Journal. 89: 465-74. PMID 15849248 DOI: 10.1529/Biophysj.104.055020 |
0.42 |
|
| 2005 |
Daidone I, Amadei A, Di Nola A. Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water. Proteins. 59: 510-8. PMID 15789436 DOI: 10.1002/Prot.20427 |
0.455 |
|
| 2005 |
Colombo G, Daidone I, Gazit E, Amadei A, Di Nola A. Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water Proteins: Structure, Function and Genetics. 59: 519-527. PMID 15778964 DOI: 10.1002/Prot.20426 |
0.424 |
|
| 2004 |
Flöck D, Daidone I, Di Nola A. A molecular dynamics study of acylphosphatase in aggregation-promoting conditions: the influence of trifluoroethanol/water solvent. Biopolymers. 75: 491-6. PMID 15526333 DOI: 10.1002/Bip.20166 |
0.379 |
|
| 2004 |
Daidone I, Simona F, Roccatano D, Broglia RA, Tiana G, Colombo G, Di Nola A. Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations. Proteins. 57: 198-204. PMID 15326604 DOI: 10.1002/Prot.20178 |
0.438 |
|
| 2004 |
Daidone I, Roccatano D, Hayward S. Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling. Journal of Molecular Biology. 339: 515-25. PMID 15147839 DOI: 10.1016/J.Jmb.2004.04.007 |
0.345 |
|
| 2003 |
Daidone I, Amadei A, Roccatano D, Nola AD. Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c. Biophysical Journal. 85: 2865-71. PMID 14581191 DOI: 10.1016/S0006-3495(03)74709-2 |
0.75 |
|
| 2003 |
Roccatano D, Daidone I, Ceruso MA, Bossa C, Di Nola A. Selective excitation of native fluctuations during thermal unfolding simulations: Horse heart cytochrome c as a case study Biophysical Journal. 84: 1876-1883. PMID 12609889 DOI: 10.1016/S0006-3495(03)74995-9 |
0.39 |
|
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