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; 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). 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  

  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; 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  

  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

  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, 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.

  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

  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.

  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  

  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.

  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.

  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.

  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  

  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  

  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

  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.; 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  

  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

  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

  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  

  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  

  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

  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

  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

  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; 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

  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  

  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  

  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  

  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