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Bernetti, Mattia

Bernetti, Mattia  

Dipartimento di Scienze Biomolecolari (DISB)  

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Titolo Data di pubblicazione Autore(i) File
Application of Deep Learning to Predict the Persistence, Bioaccumulation, and Toxicity of Pharmaceuticals 1-gen-2025 Evangelista, Dominga; Nelson, Elliot; Skyner, Rachael; Tehan, Ben; Bernetti, Mattia; Roberti, Marinella; Bolognesi, Maria Laura; Bottegoni, Giovanni
Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations 1-gen-2021 Bernetti, M.; Bussi, G.
Computational drug discovery under RNA times 1-gen-2022 Bernetti, M.; Aguti, R.; Bosio, S.; Recanatini, M.; Masetti, M.; Cavalli, A.
Data-Driven Molecular Dynamics: A Multifaceted Challenge 1-gen-2020 Bernetti, Mattia; Bertazzo, Martina; Masetti, Matteo
Enhanced Molecular Dynamics Simulations of Intrinsically Disordered Proteins 1-gen-2020 Masetti, Matteo; Bernetti, Mattia; Cavalli, Andrea
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data 1-gen-2025 Mizrahi, Orel; Corley, Meredith; Feldman, Ori; Fröhlking, Thorben; Sun, Lei; Ziesel, Alison; Antczak, Maciej; Bernetti, Mattia; Elhajjajy, Shaimae I.; Huang, Wenze; Nguyen, Grady G.; Park, Samuel S.; Perez Martell, Raul I.; Trinity, Luke; Xu, Kui; Zok, Tomasz; Bussi, Giovanni; Jabbari, Hosna; Orenstein, Yaron; Aviran, Sharon; Meyer, Michelle M.; Yeo, Gene W.
Integrating experimental data with molecular simulations to investigate RNA structural dynamics 1-gen-2023 Bernetti, M; Bussi, G
Molecular Dynamics of Solids at Constant Pressure and Stress Using Anisotropic Stochastic Cell Rescaling 1-gen-2022 Del Tatto, V.; Raiteri, P.; Bernetti, M.; Bussi, G.
Molecular Dynamics Simulations of Chemically Modified Ribonucleotides 1-gen-2023 Piomponi, Valerio; Bernetti, Mattia; Bussi, Giovanni
Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments 1-gen-2023 Calonaci, Nicola; Bernetti, Mattia; Jones, Alisha; Sattler, Michael; Bussi, Giovanni
Molecular Simulations Matching Denaturation Experiments for N-6-Methyladenosine 1-gen-2022 Piomponi, V; Froehlking, T; Bernetti, M; Bussi, G
On the allosteric puzzle and pocket crosstalk through computational means 1-gen-2023 Aguti, R; Bernetti, M; Bosio, S; Decherchi, S; Cavalli, A
Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein–Ligand to RNA-Ligand Binding 1-gen-2025 Serra, Eleonora; Ghidini, Alessia; Aguti, Riccardo; Bernetti, Mattia; Decherchi, Sergio; Cavalli, Andrea
PLUMED Tutorials: A collaborative, community-driven learning ecosystem 1-gen-2025 Tribello, Gareth A.; Bonomi, Massimiliano; Bussi, Giovanni; Camilloni, Carlo; Armstrong, Blake I.; Arsiccio, Andrea; Aureli, Simone; Ballabio, Federico; Bernetti, Mattia; Bonati, Luigi; Brookes, Samuel G. H.; Brotzakis, Z. Faidon; Capelli, Riccardo; Ceriotti, Michele; Chan, Kam-Tung; Cossio, Pilar; Dasetty, Siva; Donadio, Davide; Ensing, Bernd; Ferguson, Andrew L.; Fraux, Guillaume; Gale, Julian D.; Gervasio, Francesco Luigi; Giorgino, Toni; Herringer, Nicholas S. M.; Hocky, Glen M.; Hoff, Samuel E.; Invernizzi, Michele; Languin-Cattoën, Olivier; Leone, Vanessa; Limongelli, Vittorio; Lopez-Acevedo, Olga; Marinelli, Fabrizio; Febrer Martinez, Pedro; Masetti, Matteo; Mehdi, Shams; Michaelides, Angelos; Murtada, Mhd Hussein; Parrinello, Michele; Piaggi, Pablo M.; Pietropaolo, Adriana; Pietrucci, Fabio; Pipolo, Silvio; Pritchard, Claire; Raiteri, Paolo; Raniolo, Stefano; Rapetti, Daniele; Rizzi, Valerio; Rydzewski, Jakub; Salvalaglio, Matteo; Schran, Christoph; Seal, Aniruddha; Shayesteh Zadeh, Armin; Silva, Tomás F. D.; Spiwok, Vojtěch; Stirnemann, Guillaume; Sucerquia, Daniel; Tiwary, Pratyush; Valsson, Omar; Vendruscolo, Michele; Voth, Gregory A.; White, Andrew D.; Wu, Jiangbo
Pressure control using stochastic cell rescaling 1-gen-2020 Bernetti, Mattia; Bussi, Giovanni
Probing allosteric communication with combined molecular dynamics simulations and network analysis 1-gen-2024 Bernetti, Mattia; Bosio, Stefano; Bresciani, Veronica; Falchi, Federico; Masetti, Matteo
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles 1-gen-2021 Bernetti, Mattia; Hall, Kathleen B; Bussi, Giovanni
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin 1-gen-2024 Bosio, Stefano; Bernetti, Mattia; Rocchia, Walter; Masetti, Matteo
Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data 1-gen-2023 Fröhlking, Thorben; Bernetti, Mattia; Bussi, Giovanni
Toward empirical force fields that match experimental observables 1-gen-2020 Froehlking, Thorben; Bernetti, Mattia; Calonaci, Nicola; Bussi, Giovanni