Personal profile
Personal profile
Dr. Thomas Simonson is Professor at Ecole Polytechnique, Paris, France and a senior CNRS scientist. He is active in the development and application of computational methods, including free energy simulation techniques. He is especially interested in electrostatic interactions and structure-function relationships in biomolecules and engineering protein-ligand interactions. His early work examined dielectric relaxation in proteins, providing first principles estimates of microscopic and macroscopic susceptibilities. Subsequent work focussed on major biochemical processes where electrostatics is central, including acid/base, redox processes, and ligand binding. Since 1989, Dr. Simonson has studied protein-ligand recognition with free energy simulations, developing software, methodology, and theory. Early work used RNase S and SNase as models to understand protein stability. Subsequent work focussed on the Ras oncoprotein, its downstream target Raf, the kinases Abl and Src, translational GTPases, and several aminoacyl-tRNA synthetases. In 2005, Dr. Simonson entered the field of computational protein design (CPD), developing a large body of code, methodology, and test systems. He created the Proteins@Home distributed computing platform, which used over 30.000 volunteer computers in 100 countries (Chem Eng News, 2007).
Research interests
Education/Academic qualification
HDR (PhD Supervision Credentials)
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Collaborations and top research areas from the last five years
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Transition State-Based Computational Enzyme Design
Gaillard, T. & Simonson, T., 1 Jan 2026, Methods in Molecular Biology. Humana Press Inc., p. 165-186 22 p. (Methods in Molecular Biology; vol. 2979).Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review
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Polarizable Models for Selected Endocrine Disrupting Chemicals and Their Hosts
Mazurek, A., Thirion, V., Szeleszczuk, Ł., Piquemal, J. P., Clavaguera, C. & Simonson, T., 1 Jan 2025, (Accepted/In press) In: Journal of Computational Biophysics and Chemistry.Research output: Contribution to journal › Article › peer-review
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Classifying protein kinase conformations with machine learning
Reveguk, I. & Simonson, T., 1 Apr 2024, In: Protein Science. 33, 4, e4918.Research output: Contribution to journal › Article › peer-review
Open Access -
Uncovering substrate specificity determinants of class IIb aminoacyl-tRNA synthetases with machine learning
Simonson, T., Mihaila, V. & Reveguk, I., 1 Nov 2024, In: Journal of Molecular Graphics and Modelling. 132, 108818.Research output: Contribution to journal › Article › peer-review
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Computational protein design repurposed to explore enzyme vitality and help predict antibiotic resistance
Michael, E., Saint-Jalme, R., Mignon, D. & Simonson, T., 9 Jan 2023, In: Frontiers in Molecular Biosciences. 9, 905588.Research output: Contribution to journal › Article › peer-review
Open Access -
Enzyme redesign and genetic code expansion
Opuu, V. & Simonson, T., 1 Jan 2023, In: Protein Engineering, Design and Selection. 36, gzad017.Research output: Contribution to journal › Review article › peer-review
Open Access -
PLP-Dependent Enzyme Methionine γ-Lyase: Insights into the Michaelis Complex from Molecular Dynamics and Free Energy Simulations
Chen, X., Ferchaud, N., Briozzo, P., Machover, D. & Simonson, T., 19 Sept 2023, In: Biochemistry. 62, 18, p. 2791-2801 11 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Redesigning methionyl-tRNA synthetase for β-methionine activity with adaptive landscape flattening and experiments
Opuu, V., Nigro, G., Lazennec-Schurdevin, C., Mechulam, Y., Schmitt, E. & Simonson, T., 1 Sept 2023, In: Protein Science. 32, 9, e4738.Research output: Contribution to journal › Article › peer-review
Open Access -
A Computational Model for the PLP-Dependent Enzyme Methionine γ-Lyase
Chen, X., Briozzo, P., Machover, D. & Simonson, T., 26 Apr 2022, In: Frontiers in Molecular Biosciences. 9, 886358.Research output: Contribution to journal › Article › peer-review
Open Access -
How much can physics do for protein design?
Michael, E. & Simonson, T., 1 Feb 2022, In: Current Opinion in Structural Biology. 72, p. 46-54 9 p.Research output: Contribution to journal › Review article › peer-review
Open Access