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Journal 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 Ka'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 SimonsonJournal of Chemical Theory and Computation|September 9, 2017
Full Protein Sequence Redesign with an MMGBSA Energy FunctionThomas Gaillard, Thomas SimonsonThe Journal of Biological Chemistry|March 5, 2010
Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinasesAlexey Aleksandrov, Thomas SimonsonMethods in Molecular Biology (Clifton, N.J.)|November 1, 2025
Transition State-Based Computational Enzyme DesignThomas Gaillard, Thomas SimonsonJournal of Computational Chemistry|July 13, 2010
A large decoy set of protein-protein complexes produced by flexible dockingGuillaume Launay, Thomas SimonsonPageof 78