• 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
  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. .
• 2023
  Temmam S, Tu TC, Regnault B, Bonomi M, Chrétien D, Vendramini L, Duong TN, Phong TV, Yen NT, Anh HN, Son TH, Anh PT, Amara F, Bigot T, Munier S, Thong VD, van der Werf S, Nam VS, Eloit M, Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence., Viruses 2023 Sep; 15(9): .
• 2023
  Kende J, Bonomi M, Temmam S, Regnault B, Pérot P, Eloit M, Bigot T, Virus Pop-Expanding Viral Databases by Protein Sequence Simulation., Viruses 2023 May; 15(6): .
• 2023
  Temmam S, Montagutelli X, Herate C, Donati F, Regnault B, Attia M, Baquero Salazar E, Chretien D, Conquet L, Jouvion G, Pipoli Da Fonseca J, Cokelaer T, Amara F, Relouzat F, Naninck T, Lemaitre J, Derreudre-Bosquet N, Pascal Q, Bonomi M, Bigot T, Munier S, Rey FA, Le Grand R, van der Werf S, Eloit M, SARS-CoV-2-related bat virus behavior in human-relevant models sheds light on the origin of COVID-19., EMBO Rep 2023 Apr; 24(4): e56055.
• 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.
• 2022
  Temmam S, Vongphayloth K, Baquero E, Munier S, Bonomi M, Regnault B, Douangboubpha B, Karami Y, Chrétien D, Sanamxay D, Xayaphet V, Paphaphanh P, Lacoste V, Somlor S, Lakeomany K, Phommavanh N, Pérot P, Dehan O, Amara F, Donati F, Bigot T, Nilges M, Rey FA, van der Werf S, Brey PT, Eloit M, Bat coronaviruses related to SARS-CoV-2 and infectious for human cells., Nature 2022 Apr; 604(7905): 330-336.
• 2022
  S. Temmam, K. Vongphayloth, E. Baquero Salazar, S. Munier⋆, M. Bonomi, et al., Discovery of bat coronaviruses close to SARS-CoV-2 and infectious for human cells., Nautre 604 (2022) 330.
• 2021
  Sarah Temmam, Khamsing Vongphayloth, Eduard Baquero Salazar, Sandie Munier, Massimiliano Bonomi, Béatrice Régnault, Bounsavane Douangboubpha, Yasaman Karami, Delphine Chretien, Daosavanh Sanamxay, Vilakhan Xayaphet, Phetphoumin Paphaphanh, Vincent Lacoste, Somphavanh Somlor, Khaithong Lakeomany, Nothasin Phommavanh, Philippe Pérot, Flora Donati, Thomas Bigot, Michael Nilges, Félix Rey, Sylvie van Der Werf, Paul Brey, Marc Eloit, Coronaviruses with a SARS-CoV-2-like receptor-binding domain allowing ACE2-mediated entry into human cells isolated from bats of Indochinese peninsula, 2021.
• 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).
• 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).
• 2019
  Massimiliano Bonomi and Carlo Camilloni (eds.), Biomolecular Simulations: Methods and Protocols, Methods in Molecular Biology, vol. 2022, Humana Press (2019).
• 2019
  M. Bonomi, M. Vendruscolo, Determination of protein structural ensembles using cryo-electron microscopy, Curr. Opin. Struct. Biol. 56 (2019) 37.
• 2019
  L. Eshun-Wilson, R. Zhang, D. Portran, M. Nachury, D. Toso, T. Löhr, M. Vendruscolo, M. Bonomi, J. S. Fraser, E. Nogales, Effects of α-tubulin acetylation on microtubule structure and stability, Proc. Natl. Acad. Sci. USA 116 (2019) 10366.
• 2019
  T. Löhr, C. Camilloni, M. Bonomi, M. Vendruscolo, A practical guide to the simultaneous determination of protein structure and dynamics using metainference, Biomolecular Simulations: Methods and Protocols, Humana Press (2019).
• 2019
  Bonomi M, Hanot S, Greenberg CH, Sali A, Nilges M, Vendruscolo M, Pellarin R, Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling, Structure 27 (2019) 175-188.
• 2019
  Erika L. Buckle, Arushi Prakash, Massimiliano Bonomi, Janani Sampath, Jim Pfaendtner, Gary P. Drobny, A Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces, J. Am. Chem. Soc., 2019, 141 (5), 1998–2011.
• 2018
  Rangan R, Bonomi M, Heller GT, Cesari A, Bussi G, Vendruscolo M, Determination of Structural Ensembles of Proteins: Restraining vs Reweighting, J. Chem. Theory Comput. 2018, 14, 6632−6641.
• 2018
  Cozza C, Bonomi M, Pietropaolo A, A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes, J Chem Theory Comput 2018 Nov;14(11):5441-5445.
• 2018
  Prakash A, Fu CD, Bonomi M, Pfaendtner J, Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics, J Chem Theory Comput 2018 Oct;14(10):4985-4990.
• 2018
  Vahidi S, Ripstein ZA, Bonomi M, Yuwen T, Mabanglo MF, Juravsky JB, Rizzolo K, Velyvis A, Houry WA, Vendruscolo M, Rubinstein JL, Kay LE, Reversible inhibition of the ClpP protease via an N-terminal conformational switch, Proc. Natl. Acad. Sci. U.S.A. 2018 07;115(28):E6447-E6456.
• 2018
  Bonomi M, Pellarin R, Vendruscolo M, Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy, Biophys. J. 2018 Apr;114(7):1604-1613.
• 2018
  Heller GT, Bonomi M, Vendruscolo M, Structural Ensemble Modulation upon Small-Molecule Binding to Disordered Proteins, J. Mol. Biol. 430 (2018) 2288.
• 2018
  Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A, Integrative structure modeling with the Integrative Modeling Platform, Protein Sci. 2018 01;27(1):245-258.
• 2017
  Bonomi M, Camilloni C, Integrative structural and dynamical biology with PLUMED-ISDB, Bioinformatics 2017 Dec;33(24):3999-4000.
• 2017
  Viswanath S, Bonomi M, Kim SJ, Klenchin VA, Taylor KC, Yabut KC, Umbreit NT, Van Epps HA, Meehl J, Jones MH, Russel D, Velazquez-Muriel JA, Winey M, Rayment I, Davis TN, Sali A, Muller EG, The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling, Mol. Biol. Cell 2017 Nov;28(23):3298-3314.
• 2017
  Heller GT, Aprile FA, Bonomi M, Camilloni C, De Simone A, Vendruscolo M, Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide, J. Mol. Biol. 2017 Sep;429(18):2772-2779.
• 2017
  Sormanni P, Piovesan D, Heller GT, Bonomi M, Kukic P, Camilloni C, Fuxreiter M, Dosztanyi Z, Pappu RV, Babu MM, Longhi S, Tompa P, Dunker AK, Uversky VN, Tosatto SC, Vendruscolo M, Simultaneous quantification of protein order and disorder, Nat. Chem. Biol. 2017 03;13(4):339-342.
• 2017
  Bonomi M, Heller GT, Camilloni C, Vendruscolo M, Principles of protein structural ensemble determination, Curr. Opin. Struct. Biol. 2017 02;42:106-116.
• 2016
  Bonomi M, Camilloni C, Vendruscolo M, Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics, Sci Rep 2016 08;6:31232.
• 2016
  Yang J, Bonomi M, Calero C, Martí J, Free energy landscapes of sodium ions bound to DMPC-cholesterol membrane surfaces at infinite dilution, Phys Chem Chem Phys 2016 Apr;18(13):9036-41.
• 2016
  Bonomi M, Camilloni C, Cavalli A, Vendruscolo M, Metainference: A Bayesian inference method for heterogeneous systems, Sci Adv 2016 Jan;2(1):e1501177.
• 2015
  Zelter A, Bonomi M, Kim Jo, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN, The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling, Nat Commun 2015 Nov;6:8673.
• 2015
  Pfaendtner J, Bonomi M, Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics, J Chem Theory Comput 2015 Nov;11(11):5062-7.
• 2015
  Colas C, Grewer C, Otte NJ, Gameiro A, Albers T, Singh K, Shere H, Bonomi M, Holst J, Schlessinger A, Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening, PLoS Comput. Biol. 2015 Oct;11(10):e1004477.
• 2015
  Yang J, Calero C, Bonomi M, Martí J, Specific Ion Binding at Phospholipid Membrane Surfaces, J Chem Theory Comput 2015 Sep;11(9):4495-9.
• 2015
  Roy Choudhury A, Sikorska E, van den Boom J, Bayer P, Popenda Ł, Szutkowski K, Jurga S, Bonomi M, Sali A, Zhukov I, Passamonti S, Novič M, Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data, PLoS ONE 2015;10(8):e0135455.
• 2015
  Palazzesi F, Prakash MK, Bonomi M, Barducci A, Accuracy of current all-atom force-fields in modeling protein disordered states, J. Chem. Theory Comput. 11 (2015) 2.
• 2015
  Barducci A, Pfaendtner J, Bonomi M, Tackling sampling challenges in biomolecular simulations, Methods Mol. Biol. 2015;1215:151-71.
• 2014
  Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A, Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data, Mol. Cell Proteomics 2014 Nov;13(11):2812-23.
• 2014
  Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF, Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ, Structure 2014 Sep;22(9):1239-1251.
• 2014
  Street TO, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly MJ, Chu F, Agard DA, Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone, J. Mol. Biol. 2014 Jun;426(12):2393-404.
• 2014
  Peng LX, Hsu MT, Bonomi M, Agard DA, Jacobson MP, The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery, PLoS Comput. Biol. 2014 Feb;10(2):e1003464.
• 2014
  Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A, Modeling of proteins and their assemblies with the Integrative Modeling Platform, Methods Mol. Biol. 2014;1091:277-95.
• 2014
  G. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi, PLUMED 2: New feathers for an old bird, Comp. Phys. Comm. 185 (2014) 604.
• 2013
  Barducci A, Bonomi M, Prakash MK, Parrinello M, Free-energy landscape of protein oligomerization from atomistic simulations, Proc. Natl. Acad. Sci. U.S.A. 2013 Dec;110(49):E4708-13.
• 2013
  Waight AB, Pedersen BP, Schlessinger A, Bonomi M, Chau BH, Roe-Zurz Z, Risenmay AJ, Sali A, Stroud RM, Structural basis for alternating access of a eukaryotic calcium/proton exchanger, Nature 2013 Jul;499(7456):107-10.
• 2013
  Limongelli V, Bonomi M, Parrinello M, Funnel metadynamics as accurate binding free-energy method, Proc. Natl. Acad. Sci. U.S.A. 2013 Apr;110(16):6358-63.
• 2013
  Pedersen BP, Kumar H, Waight AB, Risenmay AJ, Roe-Zurz Z, Chau BH, Schlessinger A, Bonomi M, Harries W, Sali A, Johri AK, Stroud RM, Crystal structure of a eukaryotic phosphate transporter, Nature 2013 Apr;496(7446):533-6.
• 2012
  Schlessinger A, Wittwer MB, Dahlin A, Khuri N, Bonomi M, Fan H, Giacomini KM, Sali A, High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach, J. Biol. Chem. 2012 Nov;287(45):37745-56.
• 2012
  Deighan M, Bonomi M, Pfaendtner J, Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble, J Chem Theory Comput 2012 Jul;8(7):2189-92.
• 2011
  Pietropaolo A, Branduardi D, Bonomi M, Parrinello M, A chirality-based metrics for free-energy calculations in biomolecular systems, J Comput Chem 2011 Sep;32(12):2627-37.
• 2011
  Barducci A, Bonomi M, Derreumaux P, Assessing the Quality of the OPEP Coarse-Grained Force Field, J Chem Theory Comput 2011 Jun;7(6):1928-34.
• 2011
  A. Barducci, M. Bonomi, M. Parrinello, Metadynamics, WIREs Comput. Mol. Sci. 1 (2011) 826.
• 2010
  Bonomi M, Barducci A, Gervasio FL, Parrinello M, Multiple routes and milestones in the folding of HIV-1 protease monomer, PLoS ONE 2010 Oct;5(10):e13208.
• 2010
  Barducci A, Bonomi M, Parrinello M, Linking well-tempered metadynamics simulations with experiments, Biophys. J. 2010 May;98(9):L44-6.
• 2010
  Limongelli V, Bonomi M, Marinelli L, Gervasio FL, Cavalli A, Novellino E, Parrinello M, Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition, Proc. Natl. Acad. Sci. U.S.A. 2010 Mar;107(12):5411-6.
• 2010
  M. Bonomi, M. Parrinello, Enhanced sampling in the well-tempered ensemble, Phys. Rev. Lett. 104 (2010) 190601..
• 2009
  M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R.A. Broglia, M. Parrinello, PLUMED: A portable plugin for free-energy calculations with molecular dynamics, Comp. Phys. Comm. 180 (2009) 1961.
• 2009
  M. Bonomi, A. Barducci, M. Parrinello, Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics, J. Comp. Chem. 30 (2009) 1615..
• 2008
  Bonomi M, Branduardi D, Gervasio FL, Parrinello M, The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin, J. Am. Chem. Soc. 2008 Oct;130(42):13938-44.
• 2007
  Bonomi M, Gervasio FL, Tiana G, Provasi D, Broglia RA, Parrinello M, Insight into the folding inhibition of the HIV-1 protease by a small peptide, Biophys. J. 2007 Oct;93(8):2813-21.