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Biophysical 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 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 SimonsonJournal of Computational Chemistry|May 21, 2016
Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristicDavid Mignon, Thomas SimonsonJournal of Molecular Graphics & Modelling|November 22, 2005
Cys(x)His(y)-Zn2+ interactions: possibilities and limitations of a simple pairwise force fieldNicolas Calimet, Thomas SimonsonProteins|September 5, 2002
Cys(x)His(y)-Zn2+ interactions: thiol vs. thiolate coordinationThomas Simonson, Nicolas CalimetProteins|January 26, 2012
Conformational selection through electrostatics: Free energy simulations of GTP and GDP binding to archaeal initiation factor 2Priyadarshi Satpati, Thomas SimonsonPageof 13