PUBLICATIONS

Publication List

2024

106.  F. Catalano, D. Santorelli, A. Astegno, F. Favretto, M. D'Abramo, A. Del Giudice, M.L. De Sciscio, F. Troilo, G. Giardina, A. Di Matteo, C. Travaglini-Allocatelli

Conformational and dynamic properties of the KH1 domain of FMRP and its fragile X syndrome linked G266E variant

(2024) Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1872, 4.

105.  A. N. Nardi, A. Olivieri, M. D'Abramo*, R. Salvio

Unveiling the Cleavage Mechanism of an RNA Model Compound on the whole pH Scale: Computations Meet Experiments in the Determination of Reaction Rates

(2024) ChemPhysChem  doi.org/10.1002/cphc.202300873

104. C. G. Chen, A. Amadei, M. D’Abramo,* 

Modeling the temperature dependence of the fluorescence properties of Indole in aqueous solution

(2024) Spectrochimica Acta Part A https://doi.org/10.1016/j.saa.2024.124096.

103. A. N. Nardi, A. Olivieri, M. D’Abramo,* A. Amadei*

A theoretical-computational study of phosphodiester bond cleavage kinetics as a function of the temperature

(2024) ChemPhysChem 10.1002/cphc.202300952

102. V. G. Lui, et al.

A partial human LCK defect causes a T cell immunodeficiency with intestinal inflammation

(2024) J Exp Med 221 (1): e20230927

2023

101. M.L. De Sciscio, A. N. Nardi, F. Centola, M. Rossi, E. Guarnera, and M. D’Abramo

Molecular Modeling of the Deamidation Reaction in Solution: A Theoretical–Computational Study

J. Phys. Chem. B, 127, 44, 9550–9559

100. C. G. Chen, M.. Giustini, Marco D’Abramo, and A. Amadei

Unveiling the Excited State Dynamics of Indole in Solution

(2023) Journal of Chemical Theory and Computation 2023 DOI: 10.1021/acs.jctc.3c00221

99. V. Tedeschi, et al. 

ERAP1 and ERAP2 Haplotypes Influence Suboptimal HLA-B*27:05-Restricted Anti-Viral CD8+ T Cell Responses Cross-Reactive to Self-Epitopes

(2023) Int. J. Mol. Sci. 2023, 24(17), 13335; https://doi.org/10.3390/ijms241713335

98. D'Annibale, V., Chen, C. G., Bonomo, M., Dini, D., D'Abramo, M.,

P1 Push-Pull Dye as a Case Study in QM/MM Theoretical Characterization for Dye-sensitized Solar Cell Organic Chromophores

(2023) ChemistrySelect 2023, 8, e202204904

97. Moya, S. E., di Gianvincenzo, P. , Chotechuang, N., Boonla, C.,  D'Abramo, M, Chen, C. G., Nardi, A., Ortore, M.G., Padró, D., 

A Study of Cyanidin/Alginate Complexation: Influence of pH in Assembly and Chiral Properties

(2023)  Carbohydrate Polymers  doi:10.1016/j.carbpol.2023.120957

96. De Sciscio ML, Nardi AN, Parisi G, Bulfaro G, Costanzo A, Gugole E, Exertier C, Freda I, Savino C, Vallone B, Montemiglio LC, D'Abramo M

Effect of Salts on the Conformational Dynamics of the Cytochrome P450 OleP

(2023)  Molecules. 28(2):832. doi: 10.3390/molecules28020832

95. Nardi, A.N.; Olivieri, A.; Amadei, A.; Salvio, R.; D’Abramo, M.

Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis

(2023)  Molecules, 28, 2152  https://doi.org/10.3390/molecules28052152

94. C. G. Chen, A. N. Nardi, A. Amadei and M. D’Abramo

PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method

(2023)  JCTC 2023, https://doi.org/10.1021/acs.jctc.2c00767

2022

93. C. G. Chen, M. Aschi, M. D’Abramo and A. Amadei

A Simplified Treatment for Efficiently Modeling the Spectral Signal of Vibronic Transitions: Application to Aqueous Indole

(2022)  Molecules 2022, 27(23), 8135; https://doi.org/10.3390/molecules27238135

92. A. N. Nardi, M. D’Abramo and A. Amadei

Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases

(2022)  Molecules 2022, 27(21), 7408; https://doi.org/10.3390/molecules27217408

91. M.L. De Sciscio, V. D’Annibale and M. D’Abramo

Theoretical Evaluation of Sulfur-Based Reactions as a Model for Biological Antioxidant Defense

(2022)  IJMS 2022, 23(23), 14515 https://doi.org/10.3390/ijms232314515

90. V. D’Annibale,D. Fracassi, P. Marracino, G. D’Inzeo and M. D’Abramo

Effects of Environmental and Electric Perturbations on the pKa of Thioredoxin Cysteine 35: A Computational Study

(2022)  Molecules 2022, 27(19), 6454; https://doi.org/10.3390/molecules27196454 

89. N. Porciello, D. Cipria, G. Masi, A. Lanz, E. Milanetti, A. Grottesi, D. Howie, S. P. Cobbold, L. Schermelleh, H. He, M. D’Abramo, N. Destainville, O. Acuto, K. Nika

Role of the membrane anchor in the regulation of Lck activity

(2022)  J. Biol. Chem. https://doi.org/10.1016/j.jbc.2022.102663

88. Natalie S. Gjerde, Alessandro N. Nardi, Cheng G. Chen,  Paolo Di Gianvincenzo, Marco D’Abramo, Anita Scipioni, Luciano Galantini,  Sergio E. Moya and Mauro Giustini

Complexation and organization of doxorubicin on polystyrene sulfonate chains: impacts on doxorubicin dimerization and quenching

(2022)  PCCP DOI: 10.1039/d2cp02714c

87. N. Balasco, A. Paladino, G. Graziano, M. D’Abramo, and L. Vitagliano

Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs

(2022) J. Chem. Inf. Mod. 62, 16, 3874–3884

86. Nardi, Alessandro Nicola; Olivieri Alessio; D'Abramo, Marco

Rationalizing Sequence and Conformational Effects on the Guanine Oxidation in Different DNA Conformations

(2022) J. Phys. Chem. B.  2022 https://doi.org/10.1021/acs.jpcb.2c02391

85. Chen, Cheng Giuseppe; Nardi, Alessandro Nicola; Giustini, Mauro; D'Abramo, Marco

Absorption behavior of doxorubicin hydrochloride in Visible region in different environments: a combined experimental and computational study

(2022) PhysChemChemPhys  2022,24, 12027-12035 https://doi.org/10.1039/D1CP05182B

84. A. Santilli, A. Lapi, J. Cautela, M. D'Abramo, C. G. Chen, A. Del Giudice, S. Sennato, D. Belić, V. Hugo Soto Tellini, K. Schillén, M. C. di Gregorio, L. Galantini

Bioderived, chiral and stable 1-dimensional light responsive nanostructures: Interconversion between tubules and twisted ribbons

(2022) Journal of Colloid and Interface Science https://doi.org/10.1016/j.jcis.2022.05.025

83. Josephine Alba  and Marco D’Abramo

The Full Model of the pMHC-TCR-CD3 Complex: A Structural and Dynamical Characterization of Bound and Unbound States

(2022) Cells 2022, 11(4), 668; https://doi.org/10.3390/cells11040668

82. Leonardo Bò, Edoardo Milanetti, Cheng Giuseppe Chen, Giancarlo Ruocco, Andrea Amadei, and Marco D’Abramo

Computational Modeling of the Thermodynamics of the Mesophilic and Thermophilic Mutants of Trp-Cage Miniprotein

(2022) ACS Omega Article ASAP https://doi.org/10.1021/acsomega.1c06206

81. C. G. Chen, A.N. Nardi, A. Amadei and M. D’Abramo

Theoretical Modeling of Redox Potentials of Biomolecules

(2022) Molecules, 27, 1077 https://doi.org/10.3390/molecules27031077

80. C. G. Chen, M. Giustini, A. Scipioni, A. Amadei and M. D’Abramo

Theoretical-computational modelling of the L-alanine CD spectrum in water

(2022) Computational and Theoretical Chemistry, 1209, 113591 https://doi.org/10.1016/j.comptc.2022.113591

79. L. C. Montemiglio, E. Gugole, I. Freda, C. Exertier, L. D’Auria, C.G. Chen, A.N. Nardi, G. Cerutti, G. Parisi, M. D’Abramo, C. Savino and B. Vallone 

Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics

(2022) Biomolecules 2022, 12(1), 55  https://doi.org/10.3390/biom12010055

78. Marracino P., Caramazza L., Montagna M., Ghahri R., D'Abramo M., Liberti M. ,Apollonio F.

Electric-driven membrane poration: A rationale for water role in the kinetics of pore formation

(2022)  Bioelectrochemistry, 2022, 143, 107987 10.1016/j.bioelechem.2021.107987

2021

77.  Calvo Galve, N., Abrishamkar, A., Sorrenti, A., Di Rienzo, L., Satta, M., D'Abramo, M., Coronado, E., de Mello, A.J., Mínguez Espallargas, G. and Puigmartí-Luis, J. 

Exploiting Reaction–Diffusion Conditions to Trigger Pathway Complexity in the Growth of a MOF. 

(2021) Angew. Chem. Int. Ed.. https://doi.org/10.1002/anie.202105390

76. Balasco, N., Alba, J., D'Abramo, M., Vitagliano, L.

Quaternary Structure Transitions of Human Hemoglobin: An Atomic-Level View of the Functional Intermediate States

(2021)  J. Chem. Inf. Model. 2021, 61, 8, 3988–3999 https://doi.org/10.1021/acs.jcim.1c00315

75. Alba, J.; Montagna, M.; D’Abramo, M. 

Modelling the Activation Pathways in Full-Length Src Kinase. 

(2021) Biophysica 2021, 1, 238-248. https://doi.org/10.3390/biophysica1020018

74. V. D’Annibale, A. N. Nardi, A. Amadei, and M. D’Abramo

Theoretical Characterization of the Reduction Potentials of Nucleic Acids in Solution

(2021) Journal of Chemical Theory and Computation 17 (3), 1301-1307

73.  A. Sandomenico, L. Di Rienzo, L. Calvanese, E. Iaccarino, G. D’Auria, L. Falcigno, A. Chambery, R. Russo, G. Franzoso, L. Tornatore, M. D’Abramo, M. Ruvo, E. Milanetti, D. Raimondo

Insights into the Interaction Mechanism of DTP3 with MKK7 by Using STD-NMR and Computational Approaches 

(2021) Biomedicines doi: 10.3390/biomedicines9010020 

2020

72. Salvio, R. and D'Abramo, M., 

Conformational Mobility and Efficiency in Supramolecular Catalysis. A Computational Approach to Evaluate the Performances of Enzyme Mimics. 

(2020) Eur. J. Org. Chem., 2020: 6004-6011.  

71. Alba, J.; Di Rienzo, L.; Milanetti, E.; Acuto, O.; D’Abramo, M. 

Molecular Dynamics Simulations Reveal Canonical Conformations in Different pMHC/TCR Interactions. 

(2020) Cells, 9, 942.

70. Giuseppe E. Segreto, Josephine Alba, Riccardo Salvio and Marco D’Abramo 

DNA cleavage by endonuclease I-DmoI: a QM/MM study and comparison with experimental data provide indications on the environmental effects

(2020) Theoretical Chemistry Accounts volume 139, Article number: 68.

69. Lorenzo Di Rienzo, Edoardo Milanetti, Josephine Alba and Marco D’Abramo

Quantitative Characterization of Binding Pockets and Binding Complementarity by Means of Zernike Descriptors

(2020) J. Chem. Inf. Model. 60, 3, 1390–1398

2019

68. D'Abramo, Marco, Del Galdo, Sara and Amadei, Andrea

Theoretical–computational modelling of the temperature dependence of the folding–unfolding thermodynamics and kinetics: the case of a Trp-cage.

(2019) Phys. Chem. Chem. Phys. 21(41), 23162-23168; doi: 10.1039/C9CP03303C

67. Cautela J, Severoni E, Redondo-Gómez C, di Gregorio MC, Del Giudice A, Sennato S, Angelini R, D'Abramo M, Schillén K, Galantini L. 

C-12 vs C-3 substituted bile salts: An example of the effects of substituent position and orientation on the self-assembly of steroid surfactant isomers. 

(2019) Colloids Surf B Biointerfaces. 185 110556. doi:10.1016/j.colsurfb.2019.110556. PMID: 31704607.

66. E. Iaccarino, A. Sandomenico, G. Corvino, G. Focà, V. Severino, R. Russo, A. Caporale, D. Raimondo, M. D'Abramo, J. Alba, A.Chambery, M. Ruvo

Investigating the oxidative refolding mechanism of Cripto-1 CFC domain

(2019) Int. J. Biol. Marcomol.; https://doi.org/10.1016/j.ijbiomac.2019.07.040

65. V. Tedeschi, J. Alba, F. Paladini, M. Paroli, A. Cauli, A. Mathieu, R. Sorrentino, M. D’Abramo, M. T. Fiorillo

Unusual Placement of an EBV Epitope into the Groove of the Ankylosing Spondylitis-Associated HLA-B27 Allele Allows CD8+ T Cell Activation

(2019) Cells, 8(6), 572; https://doi.org/10.3390/cells8060572

64.  E. Tasca, J. Alba, L. Galantini, M. D’Abramo, A. M. Giuliani, A. Amadei, G. Palazzo, M. Giustini,

The self-association equilibria of doxorubicin at high concentration and ionic strength characterized by fluorescence spectroscopy and molecular dynamics simulations,

(2019) Colloids Surf. A, 577, 517-522, DOI: 10.1016/j.colsurfa.2019.06.005.

63. J. Alba, E. Milanetti, M. D'Abramo 

On the activation and deactivation pathways of the Lck kinase domain: a computational study

(2019) Journal of Computer-Aided Molecular Design doi: 10.1007/s10822-019-00204-0

62. S. Del Galdo, J. Alba, A. Amadei, M. D'Abramo

Evolutionary modes in protein observable space: the case of thioredoxins

(2019) J. Mol. Evolution. DOI: 10.1007/s00239-019-09894-4

2018

61. F. Caño-Ochoa, A. Grande-García, M. Reverte-López, M. D'Abramo and S. Ramón-Maiques

Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD

(2018) J. Biol. Chem., DOI: 10.1074/jbc.RA118.005494

60. E. Milanetti, A. G. Trandafir, J. Alba, D. Raimondo and M. D’Abramo

Efficient and Accurate Modeling of Conformational Transitions in Proteins: The Case of c-Src Kinase 

(2018) J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.8b07155

59. L. Zanetti-Polzi, S. Del Galdo, I. Daidone, M. D'Abramo, V. Barone, M. Aschi and  A. Amadei

Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory

(2018) Phys. Chem. Chem. Phys., DOI:10.1039/C8CP04190C.

58. Prieto J, Redondo P, López-Méndez B, D'Abramo M, Merino N, Blanco FJ, Duchateau P, Montoya G, Molina R. 

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease. 

(2018) Sci Rep 8, 10286.

57. Gentili P., Nardi M., Antignano I., Cambise P., D'Abramo M., D'Acunzo F., Pinna A., Ussia E.

2-(Hydroxyimino)aldehydes: Photo- and Physicochemical Properties of a Versatile Functional Group for Monomer Design.

(2018) Chem. Eur. J., 24, 7683. doi: 10.1002/chem.201800059.

56. E. Tasca, M. D'Abramo, L. Galantini, A. M. Giuliani, N. V. Pavel, G. Palazzo, M. Giustini 

A Stereochemically Driven Supramolecular Polymerisation

(2018) Chem. Eur. J. 2018, 24, 8195.

55. Lettieri R., D'Abramo M., Stella L., La Bella A., Leonelli F., Giansanti L., Venanzi M., Gatto E.

Fluorescence and computational studies of thymidine phosphorylase affinity toward lipidated 5-FU derivatives.

(2018) Spectrochim Acta A Mol Biomol Spectrosc. 15;195:84-94. doi: 10.1016/j.saa.2018.01.036.

2017

54. Alba, J, Marcaida, M.J., Prieto J., Montoya, G., Molina, R., D’Abramo, M.

Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI

(2017) Journal of Computer-Aided Molecular Design. DOI:  https://doi.org/10.1007/s10822-017-0087-5

53. Del Galdo, S., Amadei, A., and D'Abramo, M.

Density discriminates between thermophilic and mesophilic proteins

(2017) Journal of biomolecular Structure & Dynamics. DOI: 10.1080/07391102.2017.1385537

52. Aschi, M., D'Abramo, M., Amadei, A.

Photoinduced electron transfer in a dichromophoric peptide: a numerical experiment

(2017) Theoretical Chemistry Accounts 135 (5) pp 1-10

2016

51. Grottesi, A., Cecconi, S. Molina, R. and D'Abramo, M.

Effect of DNA on the Conformational Dynamics of the Endonucleases I-DmoI as provided by molecular dynamics simulations

(2016) Biopolymers, DOI: https://doi.org/10.1002/bip.22933

50. D'Abramo, M., Bešker, N., Desideri, A., Levine, A.J., Melino, G., Chillemi, G.

The p53 tetramer shows an induced-fit interaction of the C-terminal domain with the DNA-binding domain

(2016) Oncogene, 35 (25), pp. 3272-3281. 

49. Chillemi, G., Pace, E., D'Abramo, M., Benfatto, M.

Equilibrium between 5- and 6-fold coordination in the first hydration shell of Cu(II)

(2016) Journal of Physical Chemistry A, 120 (22), pp. 3958-3965. 

48. Molina, R., Besker, N., Marcaida, M.J., Montoya, G., Prieto, J., D'Abramo, M.

Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics

(2016) ACS Chemical Biology, 11 (5), pp. 1401-1407. 

47. Petaccia, M., Gentili, P., Bešker, N., D'Abramo, M., Giansanti, L., Leonelli, F., La Bella, A., Gradella Villalva, D., Mancini, G.

Kinetics and mechanistic study of competitive inhibition of thymidine phosphorylase by 5-fluoruracil derivatives

(2016) Colloids and Surfaces B: Biointerfaces, 140, pp. 121-127. 

2015

46. Mauceri, A., Fracassi, A., D'Abramo, M., Borocci, S., Giansanti, L., Piozzi, A., Galantini, L., Martino, A., D'Aiuto, V., Mancini, G.

Role of the hydrophilic spacer of glucosylated amphiphiles included in liposome formulations in the recognition of Concanavalin A

(2015) Colloids and Surfaces B: Biointerfaces, 136, pp. 232-239. 

45. D'Abramo, M., Aschi, M., Amadei, A.

Theoretical calculation of the pyrene emission properties in different solvents

(2015) Chemical Physics Letters, 639, pp. 17-22. 

44. Molina, R., Marcaida, M.J., Redondo, P., Marenchino, M., Duchateau, P., D'Abramo, M., Montoya, G., Prieto, J.

Engineering a nickase on the homing endonuclease I-DmoI Scaffold

(2015) Journal of Biological Chemistry, 290 (30), pp. 18534-18544.

43. Barbany, M., Meyer, T., Hospital, A., Faustino, I., D'Abramo, M., Morata, J., Orozco, M., De La Cruz, X.

Molecular dynamics study of naturally existing cavity couplings in proteins

(2015) PLoS ONE, 10 (3), art. no. e0119978.

42. Del Galdo, S., Marracino, P., D'Abramo, M., Amadei, A.

In silico characterization of protein partial molecular volumes and hydration shells

(2015) Physical Chemistry Chemical Physics, 17 (46), pp. 31270-31277. 

2014

41. Bešker, N., Amadei, A., Dabramo, M.

Molecular mechanisms of activation in CDK2

(2014) Journal of Biomolecular Structure and Dynamics, 32 (12), pp. 1929-1935.

40. 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

(2014) Physical Chemistry Chemical Physics, 16 (38), pp. 20624-20638.

39. D'Abramo, M., Aschi, M., Amadei, A.

Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: Explicit treatment of the vibronic transitions

(2014) Journal of Chemical Physics, 140 (16), art. no. 164104.

38. D'Abramo, M., Besker, N., Chillemi, G., Grottesi, A.

Modeling conformational transitions in kinases by molecular dynamics simulations: Achievements, difficulties, and open challenges

(2014) Frontiers in Genetics, 5 (MAY), art. no. Article 128, p. 1.

2013

37. Chillemi, G., Davidovich, P., D'Abramo, M., Mametnabiev, T., Garabadzhiu, A.V., Desideri, A., Melino, G.

Molecular dynamics of the full-length p53 monomer

(2013) Cell Cycle, 12 (18), pp. 3098-3108.

36. D'Abramo, M., Castellazzi, C.L., Orozco, M., Amadei, A.

On the nature of DNA hyperchromic effect

(2013) Journal of Physical Chemistry B, 117 (29), pp. 8697-8704.

2012

35. Molina, R., Redondo, P., Stella, S., Marenchino, M., D'Abramo, M., Gervasio, F.L., Charles Epinat, J., Valton, J., Grizot, S., Duchateau, P., Prieto, J., Montoya, G.

Non-specific protein-DNA interactions control I-CreI target binding and cleavage

(2012) Nucleic Acids Research, 40 (14), pp. 6936-6945.

34. D'Abramo, M., Rabal, O., Oyarzabal, J., Gervasio, F.L.

Conformational selection versus induced fit in kinases: The case of PI3K-Iγ

(2012) Angewandte Chemie - International Edition, 51 (3), pp. 642-646.

33. D'Abramo, M., Orozco, M., Amadei, A.

2011

Effects of local electric fields on the redox free energy of single stranded DNA

(2011) Chemical Communications, 47 (9), pp. 2646-2648.

32. Muñoz, I.G., Prieto, J., Subramanian, S., Coloma, J., Redondo, P., Villate, M., Merino, N., Marenchino, M., D'Abramo, M., Gervasio, F.L., Grizot, S., Daboussi, F., Smith, J., Chion-Sotinel, I., Pâques, F., Duchateau, P., Alibés, A., Stricher, F., Serrano, L., Blanco, F.J., Montoya, G.

Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus

(2011) Nucleic Acids Research, 39 (2), pp. 729-743.

from 2010

31. Sutto, L., D'Abramo, M., Gervasio, F.L.

Comparing the efficiency of biased and unbiased molecular dynamics in reconstructing the free energy landscape of Met-enkephalin

(2010) Journal of Chemical Theory and Computation, 6 (12), pp. 3640-3646.

30. Meyer, T., D'Abramo, M., Hospital, A., Rueda, M., Ferrer-Costa, C., Pérez, A., Carrillo, O., Camps, J., Fenollosa, C., Repchevsky, D., Gelpí, J.L., Orozco, M.

MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

(2010) Structure, 18 (11), pp. 1399-1409.

29. Pons, C., D'Abramo, M., Svergun, D.I., Orozco, M., Bernadó, P., Fernández-Recio, J.

Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data

(2010) Journal of Molecular Biology, 403 (2), pp. 217-230.

28. D'Abramo, M., Di Nola, A., Amadei, A.

Kinetics of carbon monoxide migration and binding in solvated myoglobin as revealed by molecular dynamics simulations and quantum mechanical calculations

(2009) Journal of Physical Chemistry B, 113 (51), pp. 16346-16353.

27. D'Abramo, M., Aschi, M., Amadei, A.

Charge transfer equilibria of aqueous single stranded DNA

(2009) Physical Chemistry Chemical Physics, 11 (45), pp. 10614-10618.

26. García-Fandiño, R., Granja, J.R., D'Abramo, M., Orozco, M.

Theoretical characterization of the dynamical behavior and transport properties of α,γ-peptide nanotubes in solution

(2009) Journal of the American Chemical Society, 131 (43), pp. 15678-15686.

25. D'Abramo, M., Meyer, T., Bernadó, P., Pons, C., Recio, J.F., Orozco, M.

On the use of low-resolution data to improve structure prediction of proteins and protein complexes

(2009) Journal of Chemical Theory and Computation, 5 (11), pp. 3129-3137.

24. Camps, J., Carrillo, O., Emperador, A., Orellana, L., Hospital, A., Rueda, M., Cicin-Sain, D., D'Abramo, M., Gelpí, J.L., Orozco, M.

FlexServ: An integrated tool for the analysis of protein flexibility

(2009) Bioinformatics, 25 (13), pp. 1709-1710.

23. Amadei, A., D'Alessandro, M., D'Abramo, M., Aschi, M.

Theoretical characterization of electronic states in interacting chemical systems

(2009) Journal of Chemical Physics, 130 (8), art. no. 084109.

22. D'Abramo, M., Caminiti, R., Di Nola, A., Amadei, A.

What can we learn by comparing experimental and theoretical-computational X-ray scattering data?

(2009) Journal of Molecular Liquids, 144 (1-2), pp. 9-12.

21. Apollonio, F., Liberti, M., Amadei, A., Aschi, M., Pellegrino, M., D'Alessandro, M., D'Abramo, M., Di Nola, A., D'Inzeo, G.

Mixed quantum-classical methods for molecular simulations of biochemical reactions with microwave fields: The case study of myoglobin

(2008) IEEE Transactions on Microwave Theory and Techniques, 56 (11), art. no. 4657388, pp. 2511-2519.

20. Aschi, M., D'Alessandro, M., Pellegrino, M., Nola, A.D., D'Abramo, M., Amadei, A.

Intramolecular charge transfer in π-conjugated oligomers: A theoretical study on the effect of temperature and oxidation state

(2008) Theoretical Chemistry Accounts, 119 (5-6), pp. 469-476.

19. D'Abramo, M., Di Nola, A., Aschi, M., Amadei, A.

Theoretical characterization of temperature and density dependence of liquid water electronic excitation energy: Comparison with recent experimental data

(2008) Journal of Chemical Physics, 128 (2), art. no. 021103.

18. D'Abramo, M., Aschi, M., Marinelli, F., Di Nola, A., Amadei, A.

Theoretical prediction of thermodynamic equilibrium constants of chemical reactions in water

(2007) Journal of Molecular Structure: THEOCHEM, 811 (1-3), pp. 197-201.

17. Amadei, A., D'Abramo, M., Daidone, I., D'Alessandro, M., Nola, A.D., Aschi, M.

Statistical mechanical modelling of chemical reactions in complex systems: The kinetics of the Haem carbon monoxide binding-unbinding reaction in Myoglobin

(2007) Theoretical Chemistry Accounts, 117 (5-6), pp. 637-647.

16. Amadei, A., D'Abramo, M., Nola, A.D., Arcadi, A., Cerichelli, G., Aschi, M.

Theoretical study of intramolecular charge transfer in π-conjugated oligomers

(2007) Chemical Physics Letters, 434 (4-6), pp. 194-199.

15. Apollonio, F., D'Abramo, M., Liberti, M., Amadei, A., Di Nola, A., D'Inzeo, G.

Myoglobin as a case study for molecular simulations in the presence of a microwave electromagnetic field

(2006) IEEE MTT-S International Microwave Symposium Digest, art. no. 4015287, pp. 1746-1749.

14. Zazza, C., Amadei, A., Sanna, N., Grandi, A., Chillemi, G., Di Nola, A., D'Abramo, M., Aschi, M.

Theoretical modeling of the valence UV spectra of 1,2,3-triazine and uracil in solution

(2006) Physical Chemistry Chemical Physics, 8 (12), pp. 1385-1393.

13. 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

(2006) Journal of Physical Organic Chemistry, 19 (8-9), pp. 518-530.

12. D'Abramo, M., Aschi, M., Di Nola, A., Amadei, A.

On the importance of configurational sampling in theoretical calculation of electronic properties of complex molecular systems: Acetone in water

(2006) Chemical Physics Letters, 424 (4-6), pp. 289-294.

11. D'Abramo, M., Rinaldi, A.C., Bozzi, A., Amadei, A., Mignogna, G., Di Nola, A., Aschi, M.

Conformational behavior of temporin A and temporin L in aqueous solution: A computational/experimental study

(2006) Biopolymers, 81 (3), pp. 215-224.

10. D'Alessandro, M., D'Abramo, M., Paci, M., Amadei, A.

Theoretical study of the thermodynamics of a solvated peptide: Contryphan Vn

(2005) Physica Scripta T, T118, pp. 196-198.

9. Daidone, I., D'Abramo, M., Di Nola, A., Amadei, A.

Theoretical characterization of α-helix and β-hairpin folding kinetics

(2005) Journal of the American Chemical Society, 127 (42), pp. 14825-14832.

8. Amadei, A., Marinelli, F., D'Abramo, M., D'Alessandro, M., Anselmi, M., Di Nola, A., Aschi, M.

Theoretical modeling of vibroelectronic quantum states in complex molecular systems: Solvated carbon monoxide, a test case

(2005) Journal of Chemical Physics, 122 (12), art. no. 124506.

7. D'Alessandro, M., Marinelli, F., D'Abramo, M., Aschi, M., Di Nola, A., Amadei, A.

Ground and excited electronic state thermodynamics of aqueous carbon monoxide: A theoretical study

(2005) Journal of Chemical Physics, 122 (12), art. no. 124507.

6. D'Abramo, M., D'Alessandro, M., Di Nola, A., Roccatano, D., Amadei, A.

Characterization of liquid behaviour by means of local density fluctuations

(2005) Journal of Molecular Liquids, 117 (1-3), pp. 17-21.

5. D'Abramo, M., Aschi, M., Di Nola, A., Amadei, A.

Calculation of the optical rotatory dispersion of solvated alanine by means of the perturbed matrix method

(2005) Chemical Physics Letters, 402 (4-6), pp. 559-563.

4. Aschi, M., D'Abramo, M., Di Teodoro, C., Di Nola, A., Amadei, A.

Theoretical characterisation of the electronic excitation in liquid water

(2005) ChemPhysChem, 6 (1), pp. 53-58.

3. D'Abramo, M., D'Alessandro, M., Amadei, A.

On the use of the quasi-Gaussian entropy theory in the study of simulated dilute solutions

(2004) Journal of Chemical Physics, 120 (11), pp. 5226-5234.

2. Amadei, A., D'Abramo, M., Zazza, C., Aschi, M.

Electronic properties of formaldehyde in water: A theoretical study

(2003) Chemical Physics Letters, 381 (1-2), pp. 187-193.

1. D'Alessandro, M., D'Abramom, M., Brancato, G., Di Nola, A., Amadei, A.

Statistical mechanics and thermodynamics of simulated ionic solutions

(2002) Journal of Physical Chemistry B, 106 (45), pp. 11843-11848.