Thomas Simonson

21 papers Journal 21

Year	Rank	Type	Title / Venue / Authors
2020	J	`jnl`	Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power. PLoS Comput. Biol. Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Mechulam, Thomas Simonson
2019	J	`jnl`	Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems. J. Chem. Inf. Model. Antoine Charpentier, David Mignon, Sophie Barbe, Juan Cortés, Thomas Schiex, Thomas Simonson, David Allouche
2017	J	`jnl`	Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design. J. Comput. Chem. Francesco Villa, David Mignon, Savvas Polydorides, Thomas Simonson
2017	J	`jnl`	Simple models for nonpolar solvation: Parameterization and testing. J. Comput. Chem. Eleni Michael, Savvas Polydorides, Thomas Simonson, Georgios Archontis
2016	J	`jnl`	Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic. J. Comput. Chem. David Mignon, Thomas Simonson
2016	J	`jnl`	Protein: Ligand binding free energies: A stringent test for computational protein design. J. Comput. Chem. Karen Druart, Zoltan Palmai, Eyaz Omarjee, Thomas Simonson
2014	J	`jnl`	Pairwise decomposition of an MMGBSA energy function for computational protein design. J. Comput. Chem. Thomas Gaillard, Thomas Simonson
2013	J	`jnl`	Computational protein design: The proteus software and selected applications. J. Comput. Chem. Thomas Simonson, Thomas Gaillard, David Mignon, Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Savvas Polydorides, Audrey Sedano, Karen Druart, Georgios Archontis
2013	J	`jnl`	Monte carlo simulations of proteins at constant pH with generalized born solvent, flexible sidechains, and an effective dielectric boundary. J. Comput. Chem. Savvas Polydorides, Thomas Simonson
2013	J	`jnl`	Simulating GTP: Mg and GDP: Mg with a simple force field: A structural and thermodynamic analysis. J. Comput. Chem. Thomas Simonson, Priyadarshi Satpati
2011	J	`jnl`	A large decoy set of protein-protein complexes produced by flexible docking. J. Comput. Chem. Guillaume Launay, Thomas Simonson
2010	J	`jnl`	A molecular mechanics model for imatinib and imatinib: kinase binding. J. Comput. Chem. Alexey Aleksandrov, Thomas Simonson
2010	J	`jnl`	Computational design of protein-ligand binding: Modifying the specificity of asparaginyl-tRNA synthetase. J. Comput. Chem. Anne Lopes, Marcel Schmidt am Busch, Thomas Simonson
2009	J	`jnl`	Molecular mechanics models for tetracycline analogs. J. Comput. Chem. Alexey Aleksandrov, Thomas Simonson
2008	J	`jnl`	Computational protein design: Software implementation, parameter optimization, and performance of a simple model. J. Comput. Chem. Marcel Schmidt am Busch, Anne Lopes, David Mignon, Thomas Simonson
2008	J	`jnl`	Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. BMC Bioinform. Guillaume Launay, Thomas Simonson
2008	J	`jnl`	Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design. BMC Bioinform. Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Christine Bathelt, Thomas Simonson
2007	J	`jnl`	Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets. BMC Bioinform. Guillaume Launay, Raul Mendez, Shoshana J. Wodak, Thomas Simonson
2006	J	`jnl`	The tetracycline: Mg2+ complex: A molecular mechanics force field. J. Comput. Chem. Alexey Aleksandrov, Thomas Simonson
2001	J	`jnl`	Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time-dependent charges. J. Comput. Chem. Siegfried Höfinger, Thomas Simonson
1999	J	`jnl`	Implicit solvent models: Combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect. J. Comput. Chem. François Wagner, Thomas Simonson