Thomas Simonson

Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 20

Top Venues

Protein science : a publication of the Protein Society

The journal of physical chemistry. A

Journal of chemical theory and computation

The Journal of chemical physics

CNRS

Université de Paris-Sud (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

CNRS Sep 01 2007

France

research director 1st class :: Life Science

Ecole Polytechnique Jun 01 2003

France

professor :: Biology

Education History

Université de Paris-Sud Sep 01 1982 - Jul 01 1985

France

PHD :: Condensed matter physics

Publications

Ivan Reveguk, Thomas Simonson
Classifying protein kinase conformations with machine learning. Protein science : a publication of the Protein Society 33 (4) (2024)
Ivan Reveguk, Thomas Simonson
Classifying protein kinase conformations with machine learning. Protein science : a publication of the Protein Society 33 (4) (2024)
Ivan Reveguk, Thomas Simonson
Classifying protein kinase conformations with machine learning. Protein science : a publication of the Protein Society 33 (4) (2024)
Vaitea Opuu, Giuliano Nigro, Christine Lazennec-Schurdevin, Yves Mechulam, Emmanuelle Schmitt, Thomas Simonson
Redesigning methionyl-tRNA synthetase for β-methionine activity with adaptive landscape flattening and experiments. Protein science : a publication of the Protein Society (2023)
Xingyu Chen, Nathan Ferchaud, Pierre Briozzo, David Machover, Thomas Simonson
PLP-Dependent Enzyme Methionine γ-Lyase: Insights into the Michaelis Complex from Molecular Dynamics and Free Energy Simulations. Biochemistry (2023)
Eleni Michael, Savvas Polydorides, Thomas Simonson, Georgios Archontis
Hybrid MC/MD for protein design. The Journal of chemical physics 153 (5) (2021)
Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Mechulam, Thomas Simonson
Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power. PLoS computational biology 16 (1) (2020)
David Mignon, Karen Druart, Eleni Michael, Vaitea Opuu, Savvas Polydorides, Francesco Villa, Thomas Gaillard, Nicolas Panel, Georgios Archontis, Thomas Simonson
Physics-Based Computational Protein Design: An Update. The journal of physical chemistry. A 124 (51) (2020)
Anna Helena Mazurek, Łukasz Szeleszczuk, Thomas Simonson, Dariusz Maciej Pisklak
Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens. International journal of molecular sciences 21 (17) (2020)
Francesco Villa, Alexander D MacKerell, Benoı T Roux, Thomas Simonson
Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2+". The journal of physical chemistry. A 123 (2) (2019)
Antoine Charpentier, David Mignon, Sophie Barbe, Juan Cortes, Thomas Schiex, Thomas Simonson, David Allouche
Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems. Journal of chemical information and modeling 59 (1) (2018)
Francesco Villa, Alexander D MacKerell, Benoı T Roux, Thomas Simonson
Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2. The journal of physical chemistry. A 122 (29) (2018)
Francesco Villa, Thomas Simonson
Protein p Ka's from Adaptive Landscape Flattening Instead of Constant-pH Simulations. Journal of chemical theory and computation 14 (12) (2018)
Francesco Villa, Nicolas Panel, Xingyu Chen, Thomas Simonson
Adaptive landscape flattening in amino acid sequence space for the computational design of protein:peptide binding. The Journal of chemical physics 149 (7) (2018)
Francesco Villa, David Mignon, Savvas Polydorides, Thomas Simonson
Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design. Journal of computational chemistry 38 (28) (2017)
David Mignon, Nicolas Panel, Xingyu Chen, Ernesto J Fuentes, Thomas Simonson
Computational Design of the Tiam1 PDZ Domain and Its Ligand Binding. Journal of chemical theory and computation 13 (5) (2017)
Thomas Gaillard, Thomas Simonson
Full Protein Sequence Redesign with an MMGBSA Energy Function. Journal of chemical theory and computation 13 (10) (2017)
Eleni Michael, Savvas Polydorides, Thomas Simonson, Georgios Archontis
Simple models for nonpolar solvation: Parameterization and testing. Journal of computational chemistry 38 (29) (2017)
Vaitea Opuu, Martin Silvert, Thomas Simonson
Computational design of fully overlapping coding schemes for protein pairs and triplets. Scientific reports 7 (1) (2017)
Thomas Simonson, Gerhard Hummer, Benoît Roux
Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies. The journal of physical chemistry. A 121 (7) (2017)

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Publication Activity (10 Years)

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Thomas Simonson