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The Journal of Chemical Physics|December 3, 2008
Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustnessJosselin Noirel, 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 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 Computational Chemistry|December 19, 2009
A molecular mechanics model for imatinib and imatinib:kinase bindingAlexey Aleksandrov, 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 CalimetJournal of Computational Chemistry|July 11, 2008
Molecular mechanics models for tetracycline analogsAlexey Aleksandrov, Thomas SimonsonJournal of Computational Chemistry|July 19, 2006
The tetracycline: Mg2+ complex: a molecular mechanics force fieldAlexey Aleksandrov, Thomas SimonsonProteins|January 26, 2012
Conformational selection through electrostatics: Free energy simulations of GTP and GDP binding to archaeal initiation factor 2Priyadarshi Satpati, Thomas SimonsonPageof 16