• 2025
  Holoubek J, Salát J, Matkovic M, Bednář P, Novotný P, Hradilek M, Majerová T, Rosendal E, Eyer L, Fořtová A, Beránková M, Bell-Sakyi L, Överby AK, Cavalli A, Bonomi M, Rey FA, Růžek D, Irreversible furin cleavage site exposure renders immature tick-borne flaviviruses fully infectious., Nat Commun 2025 Aug; 16(1): 7491.
• 2024
  Panei FP, Gkeka P, Bonomi M, Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN., Nat Commun 2024 Jul; 15(1): 5725.
• 2024
  Mareuil F, Moine-Franel A, Kar A, Nilges M, Ciambur CB, Sperandio O, Protein interaction explorer (PIE): a comprehensive platform for navigating protein-protein interactions and ligand binding pockets., Bioinformatics 2024 Jul; 40(7): .
• 2024
  Alexandra Moine-Franel, Fabien Mareuil, Michael Nilges, Constantin Bogdan Ciambur, Olivier Sperandio, A comprehensive dataset of protein-protein interactions and ligand binding pockets for advancing drug discovery, Scientific Data , 2024, 11 (1), pp.402. ⟨10.1038/s41597-024-03233-z⟩.
• 2024
  Hoff SE#, Zinke M#, Izadi-Pruneyre N*, Bonomi M*., Bonds and bytes: The odyssey of structural biology, Curr Opin Struct Biol. 2024 Feb;84:102746. doi: 10.1016/j.sbi.2023.102746. .
• 2022
  Zacharias Faidon Brotzakis, Thomas Löhr, Steven Truong, Samuel E Hoff, Massimiliano Bonomi, Michele Vendruscolo, Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy, bioRxiv 2022 10.1101/2022.05.29.493873.
• 2022
  Francesco Paolo Panei, Rachel Torchet, Herve Menager, Paraskevi Gkeka, Massimiliano Bonomi, HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design, bioRxiv (2022) 10.1101/2022.05.17.492306.
• 2022
  Keino Hutchinson, Dina Buitrago Silva, Joshua Bohlke, Chase Clausen, Allen A. Thomas, Massimiliano Bonomi, Avner Schlessinger, Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations, bioRxiv (2022) 10.1101/2022.05.03.490502.
• 2022
  Avner Schlessinger, Massimiliano Bonomi , Artificial Intelligence: Exploring the conformational diversity of proteins, eLife 2022;11:e78549.
• 2021
  Mallet V, Checa Ruano L, Moine Franel A, Nilges M, Druart K, Bouvier G, Sperandio O, InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions., Bioinformatics 2022 Feb; 38(5): 1261-1268.
• 2021
  Rachel-Ann A. Garibsingh, Elias Ndaru, Alisa A. Garaeva, Yueyue Shi, Laura Zielewicz, Paul Zakrepine, Massimiliano Bonomi, Dirk J. Slotboom, Cristina Paulino, Christof Grewer, and Avner Schlessinger, Rational design of ASCT2 inhibitors using an integrated experimental-computational approach, Proc. Natl. Acad. Sci. USA 118 (2021) e21040931188.
• 2021
  Mariagrazia Fortino, Concetta Cozza, Massimiliano Bonomi, Adriana Pietropaolo, Multi-replica biased sampling for photoisomerization processes in conjugated polymers, J. Chem. Phys. 154, 174108 (2021).
• 2021
  Torchet R, Druart K, Ruano LC, Moine-Franel A, Borges H, Doppelt-Azeroual O, Brancotte B, Mareuil F, Nilges M, Ménager H, Sperandio O, The iPPI-DB initiative: a community-centered database of protein-protein interaction modulators., Bioinformatics 2021 Apr; 37(1): 89-96.
• 2020
  G. T. Heller, F. A. Aprile, T. C. T. Michaels, R. Limbocker, M. Perni, F. S. Ruggeri, B. Mannini, T. Löhr, M. Bonomi, A. De Simone, I. C. Felli, R. Pierattelli, T. P. J. Knowles, C. M. Dobson, M. Vendruscolo, Small molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease, Sci. Adv. 6, eabb5924 (2020).
• 2020
  James S. Fraser, Kresten Lindorff-Larsen, Massimiliano Bonomi, What will computational modelling approaches have to say in the era of atomistic cryo-EM data?, J. Chem. Inf. Model. 2020, 60, 5, 2410–2412.
• 2019
  The PLUMED consortium, Promoting transparency and reproducibility in enhanced molecular simulations, Nature Methods 16, 670–673 (2019).