Casoria, Michele; Macchiagodena, Marina; Rovero, Paolo; Andreini, Claudia; Papini, Anna Maria; Cardini, Gianni; Pagliai, Marco (2024). Upgrading of the general AMBER force field 2 for fluorinated alcohol biosolvents: A validation for water solutions and melittin solvation. JOURNAL OF PEPTIDE SCIENCE, pp. 1-12, ISSN:1099-1387 DOI   Accesso ONLINE all'editore

  Casoria, Michele; Macchiagodena, Marina; Bazzicalupi, Carla; Andreini, Claudia; Cardini, Gianni; Papini, Anna Maria; Pagliai, Marco (2024). Machine Learning Reveals Structural Properties of Monosaccharides and their Peptide Conjugates. In: European Peptide Symposium, Michal Lebl, pp. 1278-1278. DOI  

  Di Paco, Giorgio; Macchiagodena, Marina; Procacci, Piero (2024). Identification of Potential inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand   Design, Molecular Docking and Nonequilibrium Alchemical Simulations. CHEMMEDCHEM, vol. .., pp. 1-10, ISSN:1860-7187 DOI  

  Macchiagodena, Marina; Fragai, Marco; Gallo, Angelo; Pagliai, Marco; Ravera, Enrico (2024). The Role of Lysozyme in the Formation of Bioinspired Silicon Dioxide. CHEMISTRY-A EUROPEAN JOURNAL, vol. 30, pp. 0-0, ISSN:0947-6539 DOI  

  Casoria, Michele; Macchiagodena, Marina; Bazzicalupi, Carla; Andreini, Claudia; Cardini, Gianni; Papini, Anna Maria; Pagliai, Marco (2024). An Advanced Database for GlycoPeptide Structure Exploration to build GlycoPeptideStructure Hub: GPS Hub. In: Proceedings of the 37th European Peptide Symposium, Michal Lebl, pp. 1277-1277. DOI  

  Macchiagodena, Marina; Pagliai, Marco; Procacci, Piero (2023). NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes. JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. ..., pp. 1-10, ISSN:1096-987X DOI  

  Vettori Irene, Macchiagodena Marina, Bassu Gavino, Pagliai Marco, Fratini Emiliano, Baglioni Piero (2022). Conformational and solvent effects in structural and spectroscopic properties of 2-hydroxyethyl methacrylate and acrylic acid. JOURNAL OF MOLECULAR LIQUIDS, vol. 360, pp. 0-0, ISSN:0167-7322 DOI   Accesso ONLINE all'editore

  Vettori Irene, Macchiagodena Marina, Bassu Gavino, Fratini Emiliano, Pagliai Marco, Baglioni Piero (2022). From HEMA monomers to poly-HEMA systems simulations. In: XXXVIII Reunión Bienal de la Real Sociedad Española de Química, Granada (Spagna), 27-30/06/2022, Real Sociedad Española de Química, pp. 0-0.

  Macchiagodena, Marina; Pagliai, Marco; Procacci, Piero (2022). Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease. JOURNAL OF MOLECULAR GRAPHICS & MODELLING, vol. 110, pp. 108042-108050, ISSN:1093-3263 DOI  

  Macchiagodena, Marina; Bassu, Gavino; Vettori, Irene; Fratini, Emiliano; Procacci, Piero; Pagliai, Marco (2022). 2-Butanol Aqueous Solutions: A Combined Molecular Dynamics and Small/Wide-Angle X-ray Scattering Study. JOURNAL OF PHYSICAL CHEMISTRY. A, MOLECULES, SPECTROSCOPY, KINETICS, ENVIRONMENT, & GENERAL THEORY, vol. 126, pp. 8826-8833, ISSN:1089-5639 DOI   Accesso ONLINE all'editore

  Michele Casoria, Paolo Rovero, Cardini Gianni, Marina Macchiagodena, Anna Maria Papini, Claudia Andreini, Marco Pagliai. (2022). From a bioinformatic approach to synthetic conformational peptide epitopes to disclose molecular mechanism of aberrant glucosylation in Multiple Sclerosis. In: 36th European and 12th International Peptide Symposium EPS 2022, Sitges, 28th August to 2nd September 2022, Michal Lebl, pp. 237-240.

  Casoria Michele, Rovero Paolo, Cardini Gianni, Macchiagodena Marina, Papini Anna Maria, Andreini Claudia, Pagliai Marco. (2022). From a bioinformatic approach to synthetic conformational peptide epitopes to disclose molecular mechanism of aberrant glucosylation in Multiple Sclerosis. In: workshop DCTC 2022, Florence, 8th April, none, pp. 20-21. Accesso ONLINE all'editore

  Vettori Irene, Macchiagodena Marina, Pagliai Marco, Bassu Gavino, Fratini Emiliano, Baglioni Piero (2022). Water role in hydrogels: from solvent-monomer interactions to water states in poly-HEMA systems. In: WORKSHOP DELLA DIVISIONE DI CHIMICA TEORICA E COMPUTAZIONALE - DCTC 2022, Firenze, 08/04/2022, Divisione di Chimica Teorica e Computazionale, pp. 0-0.

  Vettori Irene, Bassu Gavino, Macchiagodena Marina, Fratini Emiliano, Pagliai Marco (2022). Monomeric 2-hydroxyethyl methacrylate (HEMA) and acrylic acid (AA): structural influences on solute-solvent interactions and spectroscopic properties. In: PhD in Chemical Sciences at UniFi - PiCSU Symposium, 19-21/01/2022, Anna Maria Papini, Martina Vizza, Gina Elena Giacomazzo, Saul Santini, Marco Bonechi, Mert Acar, Davide Ranieri, Mariagrazia Lettieri, Debora Pratesi, pp. 0-0.

  Casoria Michele, Rovero Paolo, Cardini Gianni, Macchiagodena Marina, Papini Anna Maria, Andreini Claudia, Pagliai Marco (2022). Molecular Dynamic approach on synthetic conformational peptides to detect epitopes in autoimmune desease.. In: 4th National Congress of Italian Peptide Society, none, pp. 21-21.

  Del Frate G.; Macchiagodena M.; Akhunzada M.J.; D'Autilia F.; Catte A.; Bhattacharjee N.; Barone V.; Cardarelli F.; Brancato G. (2022). Probing Liquid-Ordered and Disordered Phases in Lipid Model Membranes: A Combined Theoretical and Spectroscopic Study of a Fluorescent Molecular Rotor. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 126, pp. 480-491, ISSN:1520-6106 DOI  

  Gellini C.; Macchiagodena M.; Pagliai M. (2021). Adsorption geometry of alizarin on silver nanoparticles: A computational and spectroscopic study. NANOMATERIALS, vol. 11, pp. 860-860, ISSN:2079-4991 DOI  

  Marina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, Guido Guarnieri, Francesco Iannone, Piero Procacci (2021). Nonequilibrium Alchemical Simulations for the Development of Drugs Against Covid-19. In: Marina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, Guido Guarnieri, Francesco Iannone, Piero Procacci. Methods in Pharmacology and Toxicology, pp. 1-41, New York, NY.: Springer Nature. Accesso ONLINE all'editore

  Subak H.; Selvolini G.; Macchiagodena M.; Ozkan-Ariksoysal D.; Pagliai M.; Procacci P.; Marrazza G. (2021). Mycotoxins aptasensing: From molecular docking to electrochemical detection of deoxynivalenol. BIOELECTROCHEMISTRY, vol. 138, pp. 107691-107691, ISSN:1567-5394 DOI  

  Vettori Irene, Bassu Gavino, Macchiagodena Marina, Pagliai Marco, Fratini Emiliano (2021). Hydrogels improvements through freeze-casting and anti-freezing additives. In: ACS Fall 2021, 22-26/08/2021, ACS, pp. 0-0. Accesso ONLINE all'editore

  Piero Procacci, Marina Macchiagodena, Marco Pagliai (2021). HPC-DRIVEN HIT-TO-LEAD PROCESS FOR SARS-COV-2 MAIN PROTEASE INHIBITION. In: Piero Procacci, Marina Macchiagodena1,Maurice Karrenbrock2, Marco Pagliai , Guido Guarnieri, Francesco Iannone. ENEA CRESCO in the fight against COVID-19, pp. 32-43, Roma (Italy): ENEA, ISBN:978-88-8286-415-6. Accesso ONLINE all'editore

  Macchiagodena M.; Karrenbrock M.; Pagliai M.; Procacci P. (2021). Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS. JOURNAL OF CHEMICAL INFORMATION AND MODELING, vol. 61, pp. 5320-5326-53260.1021/acs.jcim.1c00909, ISSN:1549-9596 DOI  

  Procacci, Piero; Macchiagodena, Marina (2021). On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, pp. 1-11, ISSN:0920-654X DOI   Accesso ONLINE all'editore

  Macchiagodena M.; Pagliai M.; Procacci P. (2020). Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling. CHEMICAL PHYSICS LETTERS, vol. 750, pp. 137489-137489, ISSN:0009-2614 DOI  

  Macchiagodena, Marina; Pagliai, Marco; Karrenbrock, Maurice; Guarnieri, Guido; Iannone, Francesco; Procacci, Piero (2020). Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. .., pp. 1-13, ISSN:1549-9618 DOI   Accesso ONLINE all'editore

  Procacci P.; Macchiagodena M.; Pagliai M.; Guarnieri G.; Iannone F. (2020). Interaction of hydroxychloroquine with SARS-CoV2 functional proteins using all-atoms non-equilibrium alchemical simulations. CHEMICAL COMMUNICATIONS, vol. 56, pp. 8854-8856, ISSN:1359-7345 DOI  

  Macchiagodena M.; Pagliai M.; Andreini C.; Rosato A.; Procacci P. (2020). Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. ACS OMEGA, vol. 5, pp. 15301-15310, ISSN:2470-1343 DOI  

  Pagliai M.; Macchiagodena M.; Procacci P.; Cardini G. (2019). Evidence of a Low-High Density Turning Point in Liquid Water at Ordinary Temperature under Pressure: A Molecular Dynamics Study. THE JOURNAL OF PHYSICAL CHEMISTRY LETTERS, vol. 10, pp. 6414-6418, ISSN:1948-7185 DOI   Accesso ONLINE all'editore

  Giovannini T.; Macchiagodena M.; Ambrosetti M.; Puglisi A.; Lafiosca P.; Lo Gerfo G.; Egidi F.; Cappelli C. (2019). Simulating vertical excitation energies of solvated dyes: From continuum to polarizable discrete modeling. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, vol. 119, pp. 0-0, ISSN:0020-7608 DOI  

  MacChiagodena M.; Pagliai M.; Andreini C.; Rosato A.; Procacci P. (2019). Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands. JOURNAL OF CHEMICAL INFORMATION AND MODELING, vol. 59, pp. 3803-3816, ISSN:1549-9596 DOI   Accesso ONLINE all'editore

  Egidi F.; Lo Gerfo G.; Macchiagodena M.; Cappelli C. (2018). On the nature of charge-transfer excitations for molecules in aqueous solution: a polarizable QM/MM study. THEORETICAL CHEMISTRY ACCOUNTS, vol. 137, pp. 0-0, ISSN:1432-881X DOI  

  Macchiagodena, Marina; Mancini, Giordano; Pagliai, Marco; Cardini, Gianni; Barone, Vincenzo (2018). New atomistic model of pyrrole with improved liquid state properties and structure. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, vol. 118, pp. e25554-e25554, ISSN:0020-7608 DOI   Accesso ONLINE all'editore

  Macchiagodena, Marina; Del Frate, Gianluca; Brancato, Giuseppe; Chandramouli, Balasubramanian; Mancini, Giordano; Barone, Vincenzo (2017). Computational study of the DPAP molecular rotor in various environments: from force field development to molecular dynamics simulations and spectroscopic calculations. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 19, pp. 30590-30602, ISSN:1463-9076 DOI  

  Macchiagodena, Marina; Mancini, Giordano; Pagliai, Marco; Del Frate, Gianluca; Barone, Vincenzo (2017). Fine-tuning of atomic point charges: Classical simulations of pyridine in different environments. CHEMICAL PHYSICS LETTERS, vol. 677, pp. 120-126, ISSN:0009-2614 DOI   Accesso ONLINE all'editore

  Campetella M.; Macchiagodena M.; Gontrani L.; Kirchner B. (2017). Effect of alkyl chain length in protic ionic liquids: an AIMD perspective. MOLECULAR PHYSICS, vol. 115, pp. 1582-1589, ISSN:0026-8976 DOI  

  Macchiagodena, Marina; Mancini, Giordano; Pagliai, Marco; Barone, Vincenzo (2016). Accurate prediction of bulk properties in hydrogen bonded liquids: amides as case studies. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 18, pp. 25342-25354, ISSN:1463-9076 DOI  

  Russina O.; Macchiagodena M.; Kirchner B.; Mariani A.; Aoun B.; Russina M.; Caminiti R.; Triolo A. (2015). Association in ethylammonium nitrate-dimethyl sulfoxide mixtures: First structural and dynamical evidences. JOURNAL OF NON-CRYSTALLINE SOLIDS, vol. 407, pp. 333-338, ISSN:0022-3093 DOI  

  Holloczki O.; Macchiagodena M.; Weber H.; Thomas M.; Brehm M.; Stark A.; Russina O.; Triolo A.; Kirchner B. (2015). Triphilic Ionic-Liquid Mixtures: Fluorinated and Non-fluorinated Aprotic Ionic-Liquid Mixtures. CHEMPHYSCHEM, vol. 16, pp. 3325-3333, ISSN:1439-4235 DOI  

  Podgorsek A.; MacChiagodena M.; Ramondo F.; Costa Gomes M.F.; Padua A.A.H. (2012). Glycine in 1-butyl-3-methylimidazolium acetate and trifluoroacetate ionic liquids: Effect of fluorination and hydrogen bonding. CHEMPHYSCHEM, vol. 13, pp. 1753-1763, ISSN:1439-4235 DOI  

  Macchiagodena M.; Ramondo F.; Triolo A.; Gontrani L.; Caminiti R. (2012). Liquid structure of 1-ethyl-3-methylimidazolium alkyl sulfates by x-ray scattering and molecular dynamics. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 116, pp. 13448-13458, ISSN:1520-6106 DOI  

  Campanelli, A.R.; Domenicano, A.; MacChiagodena, M.; Ramondo, F. (2011). Electronegativity and resonance parameters from the geometry of monosubstituted benzene rings. STRUCTURAL CHEMISTRY, vol. 22, pp. 1131-1141, ISSN:1040-0400 DOI  

  Macchiagodena, Marina; Gontrani, Lorenzo; Ramondo, Fabio; Triolo, Alessandro; Caminiti, Ruggero (2011). Liquid structure of 1-alkyl-3-methylimidazolium-hexafluorophosphates by wide angle x-ray and neutron scattering and molecular dynamics. THE JOURNAL OF CHEMICAL PHYSICS, vol. 134, pp. 144521-1-144521-14, ISSN:0021-9606 DOI