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Metainference: A Bayesian Inference Method for Heterogeneous Systems

 Massimiliano Bonomi , Carlo Camilloni , Andrea Cavalli , Michele Vendruscolo
Science Advances , 2016, 2 (1), pp.e1501177
Article dans une revue hal-03135847v1
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Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN

 F P Panei , P. Gkeka , M. Bonomi
2023
Pré-publication, Document de travail pasteur-04271308v1
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Determination of Structural Ensembles of Proteins: Restraining vs Reweighting

 Ramya Rangan , Massimiliano Bonomi , Gabriella Heller , Andrea Cesari , Giovanni Bussi , et al.
Journal of Chemical Theory and Computation, 2018, 14 (12), pp.6632-6641. ⟨10.1021/acs.jctc.8b00738⟩
Article dans une revue hal-03136516v1
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Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy

 Z. Faidon Brotzakis , Thomas Löhr , Steven Truong , Samuel E. Hoff , Massimiliano Bonomi , et al.
Biochemistry, 2023, 62, pp.2407-2416. ⟨10.1021/acs.biochem.3c00010⟩
Article dans une revue hal-03834207v1
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Rational design of ASCT2 inhibitors using an integrated experimental-computational approach

 Rachel-Ann A. Garibsingh , Elias Ndaru , Alisa A. Garaeva , Yueyue Shi , Laura Zielewicz , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (37), pp.e2104093118. ⟨10.1073/pnas.2104093118⟩
Article dans une revue hal-03417486v2
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Free energy landscapes of sodium ions bound to DMPC–cholesterol membrane surfaces at infinite dilution

 Jing Yang , Jordi Martí , Massimiliano Bonomi , Carles Calero
Physical Chemistry Chemical Physics, 2016, 18 (13), pp.9036-9041. ⟨10.1039/C5CP05527J⟩
Article dans une revue hal-03135819v1
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A practical guide to the simultaneous determination of protein structure and dynamics using metainference

 Thomas Löhr , Carlo Camilloni , Massimiliano Bonomi , Michele Vendruscolo
Biomolecular Simulations, 2019
Chapitre d'ouvrage hal-03135924v1
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Ligand entry pathways control the chemical space recognized by GPR183

 Viktoria Madeline Skovgaard Kjær , Tomasz Maciej Stępniewski , Brian Medel-Lacruz , Lisa Reinmuth , Marija Ciba , et al.
Chemical Science, 2023, 14 (39), pp.10671-10683. ⟨10.1039/d2sc05962b⟩
Article dans une revue pasteur-04271324v1
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Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

 Massimiliano Bonomi , Carlo Camilloni , Michele Vendruscolo
Scientific Reports, 2016, 6, ⟨10.1038/srep31232⟩
Article dans une revue hal-03135831v1

The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

 Shruthi Viswanath , Massimiliano Bonomi , Seung Joong Kim , Trisha Davis , Andrej Sali , et al.
Molecular Biology of the Cell, 2017, 28 (23), pp.3298-3314. ⟨10.1091/mbc.E17-06-0397⟩
Article dans une revue hal-03136456v1
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Simultaneous quantification of protein order and disorder using NMR spectroscopy

 Pietro Sormanni , Damiano Piovesan , Gabriella T Heller , Massimiliano Bonomi , Predrag Kukic , et al.
Nature Chemical Biology, 2017, ⟨10.1038/nchembio.2331⟩
Article dans une revue hal-03153894v1

Reversible inhibition of the ClpP protease via an N-terminal conformational switch

 Siavash Vahidi , Zev Ripstein , Massimiliano Bonomi , Walid A. Houry , Michele Vendruscolo , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2018, 115 (28), pp.E6447-E6456. ⟨10.1073/pnas.1805125115⟩
Article dans une revue hal-03136505v1
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Effects of α-tubulin acetylation on microtubule structure and stability

 Lisa Eshun-Wilson , Rui Zhang , Didier Portran , Maxence Nachury , Dan Toso , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2019, 116 (21), pp.10366-10371. ⟨10.1073/pnas.1900441116⟩
Article dans une revue hal-03135907v1
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Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding

 Rajeswari Appadurai , Jaya Krishna Koneru , Massimiliano Bonomi , Paul Robustelli , Anand Srivastava
Journal of Chemical Theory and Computation, 2023, 19, pp.4711-4727. ⟨10.1021/acs.jctc.3c00224⟩
Article dans une revue pasteur-04271328v1
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Coronaviruses with a SARS-CoV-2-like receptor-binding domain allowing ACE2-mediated entry into human cells isolated from bats of Indochinese peninsula

 Sarah Temmam , Khamsing Vongphayloth , Eduard Baquero Salazar , Sandie Munier , Massimiliano Bonomi , et al.
2021
Pré-publication, Document de travail hal-03417488v1
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Editorial: Experiments and simulations: a pas de deux to unravel biological function

 Maya Topf , Edina Rosta , Gregory R Bowman , Massimiliano Bonomi
Frontiers in Molecular Biosciences, 2021, 8 (799406), ⟨10.3389/fmolb.2021.799406⟩
Article dans une revue hal-03417985v1

Biomolecular Simulations - Methods and Protocols

 Massimiliano Bonomi , Carlo Camilloni
2019, ⟨10.1007/978-1-4939-9608-7⟩
Ouvrages hal-03135933v1
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Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics

 Arushi Prakash , Christopher Fu , Massimiliano Bonomi , Jim Pfaendtner
Journal of Chemical Theory and Computation, 2018, 14 (10), pp.4985-4990. ⟨10.1021/acs.jctc.8b00448⟩
Article dans une revue hal-03136535v1
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Bonds and Bytes: the Odyssey of Structural Biology

 Samuel Hoff , Maximilian Carl Zinke , Nadia Izadi-Pruneyre , M Bonomi
2023
Pré-publication, Document de travail pasteur-04271321v1
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Determination of protein structural ensembles using cryo-electron microscopy

 Massimiliano Bonomi , Michele Vendruscolo
Current Opinion in Structural Biology, 2018, 56, pp.37-45. ⟨10.1016/j.sbi.2018.10.006⟩
Article dans une revue hal-03135854v1
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Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations

 Keino Hutchinson , Dina Buitrago Silva , Joshua Bohlke , Chase Clausen , Allen A. Thomas , et al.
Biophysical Journal, 2022, 121, pp.4476-4491. ⟨10.1016/j.bpj.2022.11.001⟩
Article dans une revue hal-03834205v1
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Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease

 Gabriella T Heller , Francesco A Aprile , Thomas C T Michaels , Ryan Limbocker , Michele Perni , et al.
Science Advances , 2020, 6 (45), pp.eabb5924. ⟨10.1126/sciadv.abb5924⟩
Article dans une revue hal-02999939v1
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Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces

 Erika Buckle , Arushi Prakash , Massimiliano Bonomi , Janani Sampath , Jim Pfaendtner , et al.
Journal of the American Chemical Society, 2019, 141 (5), pp.1998-2011. ⟨10.1021/jacs.8b10990⟩
Article dans une revue hal-03135860v1

Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide

 Gabriella Heller , Francesco A Aprile , Massimiliano Bonomi , Carlo Camilloni , Alfonso de Simone , et al.
Journal of Molecular Biology, 2017, 429 (18), pp.2772-2779. ⟨10.1016/j.jmb.2017.07.016⟩
Article dans une revue hal-03136480v1
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Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence

 Sarah Temmam , Tran Cong Tu , Béatrice Regnault , Massimiliano Bonomi , Delphine Chrétien , et al.
Viruses, 2023, 15 (9), pp.1897. ⟨10.3390/v15091897⟩
Article dans une revue pasteur-04228724v1
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SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19

 Sarah Temmam , Xavier Montagutelli , Cécile Herate , Flora Donati , Béatrice Regnault , et al.
EMBO Reports, 2023, 24 (4), pp.e56055. ⟨10.15252/embr.202256055⟩
Article dans une revue pasteur-04072738v1
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Bat coronaviruses related to SARS-CoV-2 and infectious for human cells

 Sarah Temmam , Khamsing Vongphayloth , Eduard Baquero , Sandie Munier , Massimiliano Bonomi , et al.
Nature, 2022, 604 (7905), pp.330-336. ⟨10.1038/s41586-022-04532-4⟩
Article dans une revue pasteur-03661247v1
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Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy

 Massimiliano Bonomi , Riccardo Pellarin , Michele Vendruscolo
Biophysical Journal, 2018, 114 (7), pp.1604-1613. ⟨10.1016/j.bpj.2018.02.028⟩
Article dans une revue pasteur-02404467v1
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What will computational modelling approaches have to say in the era of atomistic cryo-EM data?

 James S Fraser , Kresten Lindorff-Larsen , Massimiliano Bonomi
Journal of Chemical Information and Modeling, 2020, 60 (5), pp.2410-2412. ⟨10.1021/acs.jcim.0c00123⟩
Article dans une revue hal-02999942v1
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Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference

 S E Hoff , F E Thomasen , K. Lindorff-Larsen , M. Bonomi
2023
Pré-publication, Document de travail pasteur-04271312v1
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