Implicit solvent models: Combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect. - François Wagner; Thomas Simonson (J. Comput. Chem., 1999)

Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time-dependent charges. - Siegfried Höfinger; Thomas Simonson (J. Comput. Chem., 2001)

The tetracycline: Mg2+ complex: A molecular mechanics force field. - Alexey Aleksandrov; Thomas Simonson (J. Comput. Chem., 2006)

Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets. - Guillaume Launay; Raul Mendez; Shoshana J. Wodak; Thomas Simonson (BMC Bioinform., 2007)

Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design. - Marcel Schmidt am Busch; Anne Lopes; Najette Amara; Christine Bathelt; Thomas Simonson (BMC Bioinform., 2008)

Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. - Guillaume Launay; Thomas Simonson (BMC Bioinform., 2008)

Computational protein design: Software implementation, parameter optimization, and performance of a simple model. - Marcel Schmidt am Busch; Anne Lopes; David Mignon; Thomas Simonson (J. Comput. Chem., 2008)

Molecular mechanics models for tetracycline analogs. - Alexey Aleksandrov; Thomas Simonson (J. Comput. Chem., 2009)

A molecular mechanics model for imatinib and imatinib: kinase binding. - Alexey Aleksandrov; Thomas Simonson (J. Comput. Chem., 2010)

Computational design of protein-ligand binding: Modifying the specificity of asparaginyl-tRNA synthetase. - Anne Lopes; Marcel Schmidt am Busch; Thomas Simonson (J. Comput. Chem., 2010)

A large decoy set of protein-protein complexes produced by flexible docking. - Guillaume Launay; Thomas Simonson (J. Comput. Chem., 2011)

Monte carlo simulations of proteins at constant pH with generalized born solvent, flexible sidechains, and an effective dielectric boundary. - Savvas Polydorides; Thomas Simonson (J. Comput. Chem., 2013)

Computational protein design: The proteus software and selected applications. - Thomas Simonson; Thomas Gaillard; David Mignon; Marcel Schmidt am Busch; Anne Lopes; Najette Amara; Savvas Polydorides; Audrey Sedano; Karen Druart; Georgios Archontis (J. Comput. Chem., 2013)

Simulating GTP: Mg and GDP: Mg with a simple force field: A structural and thermodynamic analysis. - Thomas Simonson; Priyadarshi Satpati (J. Comput. Chem., 2013)

Pairwise decomposition of an MMGBSA energy function for computational protein design. - Thomas Gaillard; Thomas Simonson (J. Comput. Chem., 2014)

Protein: Ligand binding free energies: A stringent test for computational protein design. - Karen Druart; Zoltan Palmai; Eyaz Omarjee; Thomas Simonson (J. Comput. Chem., 2016)

Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic. - David Mignon; Thomas Simonson (J. Comput. Chem., 2016)

Simple models for nonpolar solvation: Parameterization and testing. - Eleni Michael; Savvas Polydorides; Thomas Simonson; Georgios Archontis (J. Comput. Chem., 2017)

Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design. - Francesco Villa; David Mignon; Savvas Polydorides; Thomas Simonson (J. Comput. Chem., 2017)

Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems. - Antoine Charpentier; David Mignon; Sophie Barbe; Juan Cortés; Thomas Schiex; Thomas Simonson; David Allouche (J. Chem. Inf. Model., 2019)

Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power. - Vaitea Opuu; Giuliano Nigro; Thomas Gaillard; Emmanuelle Schmitt; Yves Mechulam; Thomas Simonson (PLoS Comput. Biol., 2020)