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)

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)