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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 articles
hal-03136516v1
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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
Journal articles
hal-03135847v1
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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.
2022
Preprints, Working Papers, ...
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⟩
Journal articles
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
Journal articles
hal-03135819v1
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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.
Journal articles
hal-03153894v1
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Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics
Massimiliano Bonomi
,
Carlo Camilloni
,
Michele Vendruscolo
Journal articles
hal-03135831v1
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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
Book sections
hal-03135924v1
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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.
Journal articles
hal-03136456v1
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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⟩
Journal articles
hal-03136505v1
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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 articles
hal-03136480v1
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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 articles
hal-03135860v1
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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.
Journal articles
pasteur-03661247v1
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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⟩
Journal articles
hal-03135907v1
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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
Preprints, Working Papers, ...
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
Journal articles
hal-03417985v1
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Biomolecular Simulations - Methods and Protocols
Massimiliano Bonomi
,
Carlo Camilloni
Books
hal-03135933v1
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Determination of protein structural ensembles using cryo-electron microscopy
Massimiliano Bonomi
,
Michele Vendruscolo
Journal articles
hal-03135854v1
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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 articles
hal-03136535v1
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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.
Journal articles
hal-02999939v1
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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.
2022
Preprints, Working Papers, ...
hal-03834205v1
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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.
Journal articles
pasteur-04072738v1
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Multi-replica biased sampling for photoswitchable π-conjugated polymers
Mariagrazia Fortino
,
Concetta Cozza
,
Massimiliano Bonomi
,
Adriana Pietropaolo
Journal of Chemical Physics, 2021, 154, pp.174108
Journal articles
hal-03151767v1
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Principles of protein structural ensemble determination
Massimiliano Bonomi
,
Gabriella Heller
,
Carlo Camilloni
,
Michele Vendruscolo
Journal articles
hal-03136490v1
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Structural Ensemble Modulation upon Small-Molecule Binding to Disordered Proteins
Gabriella Heller
,
Massimiliano Bonomi
,
Michele Vendruscolo
Journal articles
hal-03136492v1
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A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes
Concetta Cozza
,
Massimiliano Bonomi
,
Adriana Pietropaolo
Journal articles
hal-03136519v1
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Integrative structural and dynamical biology with PLUMED-ISDB
Massimiliano Bonomi
,
Carlo Camilloni
Journal articles
hal-03136441v1
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Simultaneous quantification of protein order and disorder
Pietro Sormanni
,
Damiano Piovesan
,
Gabriella Heller
,
Massimiliano Bonomi
,
Predrag Kukic
,
et al.
Journal articles
hal-01802823v1
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Integrative structure modeling with the Integrative Modeling Platform
Benjamin Webb
,
Shruthi Viswanath
,
Massimiliano Bonomi
,
Riccardo Pellarin
,
Charles Greenberg
,
et al.
Protein Science, 2018, Special Issue: Special Issue on Tools for Protein Science, 27 (1), pp.245-258. ⟨10.1002/pro.3311⟩
Journal articles
pasteur-02406448v1
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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 articles
hal-02999942v1
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