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Biochemistry|December 15, 2011
Conformational selection by the aIF2 GTPase: a molecular dynamics study of functional pathwaysPriyadarshi Satpati, Thomas SimonsonBMC Structural Biology|November 21, 2007
Neutral evolution of protein-protein interactions: a computational study using simple modelsJosselin Noirel, Thomas SimonsonJournal of Computational Chemistry|January 3, 2013
Simulating GTP:Mg and GDP:Mg with a simple force field: a structural and thermodynamic analysisThomas Simonson, Priyadarshi SatpatiJournal of Computational Chemistry|October 15, 2013
Monte Carlo simulations of proteins at constant pH with generalized Born solvent, flexible sidechains, and an effective dielectric boundarySavvas Polydorides, Thomas SimonsonJournal of Computational Chemistry|May 24, 2014
Pairwise decomposition of an MMGBSA energy function for computational protein designThomas Gaillard, Thomas SimonsonJournal of Chemical Theory and Computation|November 16, 2018
Protein p K<sub>a</sub>'s from Adaptive Landscape Flattening Instead of Constant-pH SimulationsFrancesco Villa, Thomas SimonsonProteins|August 14, 2012
Nucleotide recognition by the initiation factor aIF5B: free energy simulations of a neoclassical GTPaseThomas Simonson, Priyadarshi SatpatiBiophysical Journal|April 12, 2005
Proton binding to proteins: a free-energy component analysis using a dielectric continuum modelGeorgios Archontis, Thomas SimonsonThe Journal of Biological Chemistry|June 16, 2006
Molecular dynamics simulations show that bound Mg2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactionsDamien Thompson, Thomas SimonsonThe Journal of Chemical Physics|December 3, 2008
Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustnessJosselin Noirel, Thomas SimonsonPageof 39