Publications in peer-reviewed journals

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  • Determinants of neutral antagonism and inverse agonism in the β2-Adrenergic receptor

    J Calderon, I Passainte, D Gobbo, FL Gervasio, T Clark

    J. Chem. Inf. Model. 2024, 64 (6), 2045-2057

    Contribution: DG analysed the data, wrote the paper.

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  • Activation/deactivation free-energy profiles for the β2-Adrenergic receptor: Ligand modes of action

    J Calderon, I Passainte, D Gobbo, FL Gervasio, T Clark

    J. Chem. Inf. Model. 2023, 63 (20), 6332-6343

    Contribution: DG analysed the data, wrote the paper.

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  • Architecture of the MKK6-p38 complex defines the basis of MAPK specificity and activation

    P Juyoux, I Galdadas*, D Gobbo*, J von Velsen, M Pelosse, M Tully, O Vadas, FL Gervasio, E Pellegrini, M W Bowler

    Science 2023, 6663 (381), 1217-1225

    Contribution: DG analysed the data, wrote the paper.

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  • General metadynamics protocol to simulate activation/deactivation of Class A GPCRs: Proof of principles for the serotonin receptor

    J Calderon, I Passainte, D Gobbo, FL Gervasio, T Clark

    J. Chem. Inf. Model. 2023, 63 (10), 3105-3117

    Contribution: DG analysed the data, wrote the paper.

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  • Absorption of phosphonium cations and dications into a hydrated POPC phospholipid bilayer: a computational study

    VVS Pillai, P Kumari, A Benedetto, D Gobbo, P Ballone

    J. Phys. Chem. B 2022, 126 (23), 4272-4288

    Contribution: DG run the simulations, analysed the data, wrote the paper.

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  • Machine learning and enhanced sampling for computing the potential of mean force and standard binding free energy

    M Bertazzo*, D Gobbo*, S Decherchi, A Cavalli

    J. Chem. Theory Comput. 2021, 17 (8), 5287-5300

    Contribution: DG contributed to the method development, run the simulations, analysed the data, wrote the paper.

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  • Computational analysis of the effect of [TEA][MS] and [TEA][H2PO4] ionic liquids on the structure and stability of Aβ42(17-42) amyloid fibrils

    D Gobbo, A Cavalli, P Ballone, A Benedetto

    Phys. Chem. Chem. Phys. 2021, 23 (11), 6695-6709

    Contribution: DG run the simulations, analysed the data, wrote the paper.

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  • The transition from salt-in-water to water-in-salt nanostructures in water solutions of organic ionic liquids relevant for biological applications

    P Kumari, VVS Pillai, D Gobbo, P Ballone, A Benedetto

    Phys. Chem. Chem. Phys. 2021, 23 (2), 944-959

    Contribution: DG run the simulations, analysed the data, wrote the paper.

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  • Coarse-grained model of entropy-driven demixing

    D Gobbo, P Ballone, BD Garabato

    J. Phys. Chem. B 2020, 124 (41), 9267-9274

    Contribution: DG run the simulations, contributed to the method development, analysed the data, wrote the paper.

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  • The solvation advantage of amorphous ketoprofen. Thermodynamic and kinetic aspects by molecular dynamics and free energy approaches

    D Gobbo, P Ballone, S Decherchi, A Cavalli

    J. Chem. Theory Comput. 2020, 16 (7), 4126-4140

    Contribution: DG run the simulations, contributed to the method development, analysed the data, wrote the paper.

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  • Investigating drug-target residence time in kinases through enhanced sampling simulations

    D Gobbo, V Piretti, RMC Di Martino, SK Tripathi, B Giabbai, P Storici, N Demitri, S Girotto, S Decherchi, A Cavalli

    J. Chem. Theory Comput. 2019, 15 (8), 4646-4659

    Contribution: DG run the simulations, contributed to the experimental kinetic assays setup, analysed the data, wrote the paper.

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