Massimiliano Bonomi (0000-0002-7321-0004)

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Biography

My research is focused on developing and applying computational methods based on Bayesian statistics to create maximally accurate structural models of proteins and macromolecular complexes by combining noisy, sparse, ambiguous, and even low-resolution experimental data collected on conformationally heterogeneous samples. Furthermore, efficient generation of models required advanced sampling techniques, which I develop and disseminate through the PLUMED package (www.plumed.org).

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Institut Pasteur: Paris, Île-de-France, FR

2018-10-01 to present

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Massimiliano Bonomi

https://orcid.org/0000-0002-7321-0004

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Biography

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Employment (5)

Institut Pasteur: Paris, Île-de-France, FR

CNRS Délégation Ile-de-France Ouest et Nord: Meudon, Île-de-France, FR

University of Cambridge: Cambridge, Cambridgeshire, GB

University of Washington: Seattle, WA, US

University of California San Francisco: San Francisco, CA, US

Education and qualifications (3)

Sorbonne University: Paris, FR

Eidgenössische Technische Hochschule Zürich: Zurich, ZH, CH

University of Milan: Milan, IT

Professional activities (2)

Biophysical Society: Rockville, Maryland, US

Biophysical Society: Rockville, Maryland, US

Funding (6)

Integrative modelling of protein structure and dynamics with cryo-EM

CECAM school ”Open source software for enhanced-sampling simulations”

CNRS distinction for scientific research of high international level

Design and characterization of nanostructurated materials

CECAM school ”Enhancing molecular simulations with PLUMED”

Travel Award from University of Illinois at Urbana-Champaign

Works (50 of 78)

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution

Ensemble Refinement of mismodeled cryo-EM RNA Structures Using All-Atom Simulations

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference

Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN

Bonds and bytes: The odyssey of structural biology

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference

Determination of the Structure and Dynamics of the Fuzzy Coat of an Amyloid Fibril of IAPP Using Cryo-Electron Microscopy

Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN

Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding

Virus Pop—Expanding Viral Databases by Protein Sequence Simulation

Describing inhibitor specificity for the amino acid transporter LAT1 from metainference simulations

HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design

Author Correction: Bat coronaviruses related to SARS-CoV-2 and infectious for human cells

Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy

HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design

Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations

Exploring the conformational diversity of proteins

Bat coronaviruses related to SARS-CoV-2 and infectious for human cells

Coronaviruses with a SARS-CoV-2-like receptor-binding domain allowing ACE2-mediated entry into human cells isolated from bats of Indochinese peninsula

Rational design of ASCT2 inhibitors using an integrated experimental-computational approach

Multi-replica biased sampling for photoswitchable π-conjugated polymers

Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease

Structural basis for stereospecific inhibition of ASCT2 from rational design

What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data?

A practical guide to the simultaneous determination of protein structure and dynamics using metainference

Biomolecular Simulations: Methods and Protocols

Promoting transparency and reproducibility in enhanced molecular simulations

Determination of protein structural ensembles using cryo-electron microscopy

Bayesian weighing of electron cryo-microscopy data for integrative structural modeling

Effects of α-tubulin acetylation on microtubule structure and stability

Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces

A structural ensemble modulation mechanism of small molecule binding to disordered proteins

Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics

Integrative structure modeling with the Integrative Modeling Platform

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

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy

Determination of Structural Ensembles of Proteins: Restraining vs Reweighting

A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes

Integrative structural and dynamical biology with PLUMED-ISDB

Principles of protein structural ensemble determination

Sequence specificity in the entropy-driven binding of a small molecule and a disordered peptide

Simultaneous quantification of protein order and disorder

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

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy

Free energy landscapes of sodium ions bound to DMPC--cholesterol membrane surfaces at infinite dilution

Metadynamic metainference: enhanced sampling of the metainference ensemble using metadynamics

Metainference: A Bayesian inference method for heterogeneous systems

Efficient sampling of high-dimensional free-energy landscapes with parallel bias metadynamics

Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening