Publications by authors named "Thomas Simonson"

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Transition State-Based Computational Enzyme Design.
Thomas Gaillard, Thomas Simonson

Methods Mol Biol· November 2025

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An overview of basic pathophysiological interactions between gut bacteria and their host.
Mathilde Simonson, Thomas Simonson, Estelle Nobécourt

Front Nutr· September 2025

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Uncovering substrate specificity determinants of class IIb aminoacyl-tRNA synthetases with machine learning.
Thomas Simonson, Victor Mihaila, Ivan Reveguk

J Mol Graph Model· November 2024

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Classifying protein kinase conformations with machine learning.
Ivan Reveguk, Thomas Simonson

Protein Sci· April 2024

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Redesigning methionyl-tRNA synthetase for β-methionine activity with adaptive landscape flattening and experiments.
Vaitea Opuu, Giuliano Nigro, Christine Lazennec-Schurdevin, Yves Mechulam, Emmanuelle Schmitt, Thomas Simonson

Protein Sci· September 2023

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PLP-Dependent Enzyme Methionine γ-Lyase: Insights into the Michaelis Complex from Molecular Dynamics and Free Energy Simulations.
Xingyu Chen, Nathan Ferchaud, Pierre Briozzo, David Machover, Thomas Simonson

Biochemistry· September 2023

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Computational protein design repurposed to explore enzyme vitality and help predict antibiotic resistance.
Eleni Michael, Rémy Saint-Jalme, David Mignon, Thomas Simonson

Front Mol Biosci· January 2023

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Enzyme redesign and genetic code expansion.
Vaitea Opuu, Thomas Simonson

Protein Eng Des Sel· January 2023

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A Computational Model for the PLP-Dependent Enzyme Methionine -Lyase.
Xingyu Chen, Pierre Briozzo, David Machover, Thomas Simonson

Front Mol Biosci· April 2022

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Knowledge-Based Unfolded State Model for Protein Design.
Vaitea Opuu, David Mignon, Thomas Simonson

Methods Mol Biol· March 2022

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How much can physics do for protein design?
Eleni Michael, Thomas Simonson

Curr Opin Struct Biol· February 2022

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Computational Design of PDZ-Peptide Binding.
Nicolas Panel, Francesco Villa, Vaitea Opuu, David Mignon, Thomas Simonson

Methods Mol Biol· June 2021

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Physics-Based Computational Protein Design: An Update.
David Mignon, Karen Druart, Eleni Michael, Vaitea Opuu, Savvas Polydorides, Thomas Simonson

J Phys Chem A· December 2020

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Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens.
Anna Helena Mazurek, Łukasz Szeleszczuk, Thomas Simonson, Dariusz Maciej Pisklak

Int J Mol Sci· September 2020

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Hybrid MC/MD for protein design.
Eleni Michael, Savvas Polydorides, Thomas Simonson, Georgios Archontis

J Chem Phys· August 2020

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A physics-based energy function allows the computational redesign of a PDZ domain.
Vaitea Opuu, Young Joo Sun, Titus Hou, Nicolas Panel, Ernesto J Fuentes, Thomas Simonson

Sci Rep· July 2020

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Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power.
Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Mechulam, Thomas Simonson

PLoS Comput Biol· January 2020

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Differences in Outcomes Reported by Patients With Inflammatory Bowel Diseases vs Their Health Care Professionals.
Valérie E H Pittet, Michel H Maillard, Thomas Simonson, Nicolas Fournier, Gerhard Rogler

Clin Gastroenterol Hepatol· September 2019

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Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems.
Antoine Charpentier, David Mignon, Sophie Barbe, Juan Cortes, Thomas Schiex, Thomas Simonson

J Chem Inf Model· January 2019

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Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg".
Francesco Villa, Alexander D MacKerell, Benoît Roux, Thomas Simonson

J Phys Chem A· January 2019

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Protein p K's from Adaptive Landscape Flattening Instead of Constant-pH Simulations.
Francesco Villa, Thomas Simonson

J Chem Theory Comput· December 2018

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Adaptive landscape flattening in amino acid sequence space for the computational design of protein:peptide binding.
Francesco Villa, Nicolas Panel, Xingyu Chen, Thomas Simonson

J Chem Phys· August 2018

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Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg.
Francesco Villa, Alexander D MacKerell, Benoît Roux, Thomas Simonson

J Phys Chem A· July 2018

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Corrigendum: Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study.
Manjeet Kumar, Thomas Simonson, Gilles Ohanessian, Carine Clavaguéra

Chemphyschem· May 2018

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Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations.
Nicolas Panel, Francesco Villa, Ernesto J Fuentes, Thomas Simonson

Biophys J· March 2018

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