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Author Details

Massimiliano Bonomi
Institut Pasteur, Universite Paris Cite, CNRS UMR 8
2007
60
34
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36876574SARS-CoV-2-related bat virus behavior in human-relevant models sheds light on the origin of COVID-19.EMBO Rep2023
37376527Virus Pop-Expanding Viral Databases by Protein Sequence Simulation.Viruses2023
37338049Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding.J Chem Theory Comput2023
37477459Determination of the Structure and Dynamics of the Fuzzy Coat of an Amyloid Fibril of IAPP Using Cryo-Electron Microscopy.Biochemistry2023
35172323Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.Nature2022
35443909Exploring the conformational diversity of proteins.Elife2022
35798954Author Correction: Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.Nature2022
36369754Describing inhibitor specificity for the amino acid transporter LAT1 from metainference simulations.Biophys J2022
34241080Multi-replica biased sampling for photoswitchable Ï¿-conjugated polymers.J Chem Phys2021
34912853Editorial: Experiments and Simulations: A <i>Pas de Deux</i> to Unravel Biological Function.Front Mol Biosci2021
34507995Rational design of ASCT2 inhibitors using an integrated experimental-computational approach.Proc Natl Acad Sci U S A2021
33148639Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease.Sci Adv2020
32090567What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data?J Chem Inf Model2020
30502729Determination of protein structural ensembles using cryo-electron microscopy.Curr Opin Struct Biol2019
31396909A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference.Methods Mol Biol2019
31072936Effects of α-tubulin acetylation on microtubule structure and stability.Proc Natl Acad Sci U S A2019
30393052Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.Structure2019
30618247Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces.J Am Chem Soc2019
28960548Integrative structure modeling with the Integrative Modeling Platform.Protein Sci2018
29941580Reversible inhibition of the ClpP protease via an N-terminal conformational switch.Proc Natl Acad Sci U S A2018
30075630Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics.J Chem Theory Comput2018
30428663Determination of Structural Ensembles of Proteins: Restraining vs Reweighting.J Chem Theory Comput2018
30365313A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes.J Chem Theory Comput2018
29642030Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy.Biophys J2018
29596915Structural Ensemble Modulation upon Small-Molecule Binding to Disordered Proteins.J Mol Biol2018
28063280Principles of protein structural ensemble determination.Curr Opin Struct Biol2017
28328918Simultaneous quantification of protein order and disorder.Nat Chem Biol2017
28961689Integrative structural and dynamical biology with PLUMED-ISDB.Bioinformatics2017
28814505The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling.Mol Biol Cell2017
28743590Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide.J Mol Biol2017
26844300Metainference: A Bayesian inference method for heterogeneous systems.Sci Adv2016
27561930Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics.Sci Rep2016
26967312Free energy landscapes of sodium ions bound to DMPC-cholesterol membrane surfaces at infinite dilution.Phys Chem Chem Phys2016
25330963Tackling sampling challenges in biomolecular simulations.Methods Mol Biol2015
26575939Specific Ion Binding at Phospholipid Membrane Surfaces.J Chem Theory Comput2015
26574304Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics.J Chem Theory Comput2015
26574197Accuracy of current all-atom force-fields in modeling protein disordered states.J Chem Theory Comput2015
26560693The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling.Nat Commun2015
26291722Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data.PLoS One2015
26444490Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening.PLoS Comput Biol2015
24203340Modeling of proteins and their assemblies with the Integrative Modeling Platform.Methods Mol Biol2014
25087511Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ.Structure2014
25139910Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data.Mol Cell Proteomics2014
24516374The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery.PLoS Comput Biol2014
24726919Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone.J Mol Biol2014
23542591Crystal structure of a eukaryotic phosphate transporter.Nature2013
24248370Free-energy landscape of protein oligomerization from atomistic simulations.Proc Natl Acad Sci U S A2013
23685453Structural basis for alternating access of a eukaryotic calcium/proton exchanger.Nature2013
23553839Funnel metadynamics as accurate binding free-energy method.Proc Natl Acad Sci U S A2013
22932902High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach.J Biol Chem2012
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Collaborators

Michele Vendruscolo
University of Cambridge
Co-authored papers 15
Andrej Sali (CM4AI)
University of California San Francisco
Co-authored papers 11
Riccardo Pellarin
CNRS UMR 5086 and Universite Claude Bernard Lyon 1
Co-authored papers 7
Avner Schlessinger
Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai
Co-authored papers 7
Trisha N Davis
University of Washington
Co-authored papers 3
Michael Nilges
Institut Pasteur
Co-authored papers 3
Daniel Russel
University of California san francisco
Co-authored papers 3
Charles H Greenberg
University of California San Francisco
Co-authored papers 3
Michael Riffle
University of Washington
Co-authored papers 2
Shruthi Viswanath
National Center for Biological Sciences, Tata Institute of Fundamental Research
Co-authored papers 2
Bryant H Chau
Co-authored papers 2
James S Fraser
University of California san francisco
Co-authored papers 2
Andrew B Waight
Merck & Co.
Co-authored papers 2
Robert M Stroud
University of California San Francisco
Co-authored papers 2
Eric G D Muller
University of Washington
Co-authored papers 2
Seung Joong Kim
Korea Advanced Institute of Science and Technology (KAIST)
Co-authored papers 2
Aaron J Risenmay
Co-authored papers 2
Bj??rn Panyella Pedersen
Aarhus University
Co-authored papers 2
Benjamin Webb
University of California san francisco
Co-authored papers 2
Neil T Umbreit
University of Washington
Co-authored papers 2
Javier A Vel??zquez-Muriel
University of California san francisco
Co-authored papers 2
David A Agard
University of California, USA Quantitative Biosciences Institute (QBI) san francisco
Co-authored papers 2
Daniel Jaschob
University of Washington
Co-authored papers 2
Zygy Roe-Zurz
Pfizer Inc.
Co-authored papers 2
Heather L Van Epps
University of Washington
Co-authored papers 1
Emilia Sikorska
University of Gdansk
Co-authored papers 1
Michael R Hoopmann
Institute for Systems Biology
Co-authored papers 1
Michael J MacCoss
University of Washington
Co-authored papers 1
Mark Winey
University of California davis
Co-authored papers 1
Richard S Johnson
University of Washington-Genome Sciences
Co-authored papers 1
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