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)

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)

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)

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)