| Promoting transparency and reproducibility in enhanced molecular simulations Nature methods 16 (8), 670-673, 2019 | 812 | 2019 |
| Pressure control using stochastic cell rescaling M Bernetti, G Bussi The Journal of Chemical Physics 153 (11), 2020 | 295 | 2020 |
| Kinetics of drug binding and residence time M Bernetti, M Masetti, W Rocchia, A Cavalli Annual review of physical chemistry 70 (1), 143-171, 2019 | 138 | 2019 |
| Protein–ligand (un) binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling M Bernetti, A Cavalli, L Mollica MedChemComm 8 (3), 534-550, 2017 | 103 | 2017 |
| Toward empirical force fields that match experimental observables T Fröhlking, M Bernetti, N Calonaci, G Bussi The Journal of chemical physics 152 (23), 2020 | 86 | 2020 |
| Predicting residence time and drug unbinding pathway through scaled molecular dynamics DA Schuetz, M Bernetti, M Bertazzo, D Musil, HM Eggenweiler, ... Journal of Chemical Information and Modeling 59 (1), 535-549, 2018 | 74 | 2018 |
| An integrated Markov state model and path metadynamics approach to characterize drug binding processes M Bernetti, M Masetti, M Recanatini, RE Amaro, A Cavalli Journal of chemical theory and computation 15 (10), 5689-5702, 2019 | 54 | 2019 |
| Data-driven molecular dynamics: a multifaceted challenge M Bernetti, M Bertazzo, M Masetti Pharmaceuticals 13 (9), 253, 2020 | 36 | 2020 |
| Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles M Bernetti, KB Hall, G Bussi Nucleic acids research 49 (14), e84-e84, 2021 | 33 | 2021 |
| Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations M Bernetti, M Masetti, F Pietrucci, M Blackledge, MR Jensen, ... The Journal of Physical Chemistry B 121 (41), 9572-9582, 2017 | 29 | 2017 |
| Binding residence time through scaled molecular dynamics: A prospective application to hdaao inhibitors M Bernetti, E Rosini, L Mollica, M Masetti, L Pollegioni, M Recanatini, ... Journal of Chemical Information and Modeling 58 (11), 2255-2265, 2018 | 26 | 2018 |
| Integrating experimental data with molecular simulations to investigate RNA structural dynamics M Bernetti, G Bussi Current Opinion in Structural Biology 78, 102503, 2023 | 22 | 2023 |
| Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations M Bernetti, G Bussi The European Physical Journal B 94, 1-8, 2021 | 18 | 2021 |
| Development of a multisite model for Ni (II) ion in solution from thermodynamic and kinetic data M Masetti, F Musiani, M Bernetti, F Falchi, A Cavalli, S Ciurli, M Recanatini Journal of Computational Chemistry 38 (21), 1834-1843, 2017 | 13 | 2017 |
| Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine V Piomponi, T Fröhlking, M Bernetti, G Bussi ACS Central Science 8 (8), 1218-1228, 2022 | 12 | 2022 |
| Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations M Bertazzo, M Bernetti, M Recanatini, M Masetti, A Cavalli Journal of Chemical Information and Modeling 58 (2), 490-500, 2018 | 11 | 2018 |
| Computational drug discovery under RNA times M Bernetti, R Aguti, S Bosio, M Recanatini, M Masetti, A Cavalli QRB Discovery, 1-21, 2022 | 9 | 2022 |
| On the allosteric puzzle and pocket crosstalk through computational means R Aguti, M Bernetti, S Bosio, S Decherchi, A Cavalli The Journal of Chemical Physics 158 (16), 2023 | 6 | 2023 |
| Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data T Fröhlking, M Bernetti, G Bussi The Journal of Chemical Physics 158 (21), 2023 | 5 | 2023 |
| Probing allosteric communication with combined molecular dynamics simulations and network analysis M Bernetti, S Bosio, V Bresciani, F Falchi, M Masetti Current Opinion in Structural Biology 86, 102820, 2024 | 4 | 2024 |