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Scientific Reports|November 22, 2017
Computational design of fully overlapping coding schemes for protein pairs and tripletsVaitea Opuu, Martin Silvert, Thomas SimonsonAccounts of Chemical Research|June 19, 2002
Free energy simulations come of age: protein-ligand recognitionThomas Simonson, Georgios Archontis, Martin KarplusMethods in Molecular Biology (Clifton, N.J.)|March 17, 2022
Knowledge-Based Unfolded State Model for Protein DesignVaitea Opuu, David Mignon, Thomas SimonsonJournal of Molecular Recognition : JMR|August 21, 2009
Alchemical free energy simulations for biological complexes: powerful but temperamentalAlexey Aleksandrov, Damien Thompson, Thomas SimonsonThe Journal of Physical Chemistry. A|February 3, 2017
Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free EnergiesThomas Simonson, Gerhard Hummer, Benoît RouxFrontiers in Nutrition|August 28, 2025
An overview of basic pathophysiological interactions between gut bacteria and their hostMathilde Simonson, Thomas Simonson, Estelle NobécourtBiochimica Et Biophysica Acta|July 23, 2014
Electrostatic free energies in translational GTPases: Classic allostery and the restThomas Simonson, Alexey Aleksandrov, Priyadarshi SatpatiAnnual Review of Biophysics|March 13, 2019
Generalized Born Implicit Solvent Models for BiomoleculesAlexey V Onufriev, David A CaseJournal of Molecular Biology|February 21, 2006
Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pairDavid H Mathews, David A CaseProteins|March 8, 2016
Protein side chain conformation predictions with an MMGBSA energy functionThomas Gaillard, Nicolas Panel, Thomas SimonsonPageof 39