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)

Protein Structural Statistics with PSS. - Thomas Gaillard; Benjamin B. L. Schwarz; Yassmine Chebaro; Roland H. Stote; Annick Dejaegere (J. Chem. Inf. Model., 2013)

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

PSSweb: protein structural statistics web server. - Thomas Gaillard; Roland H. Stote; Annick Dejaegere (Nucleic Acids Res., 2016)

Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark. - Thomas Gaillard (J. Chem. Inf. Model., 2018)

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)

Towards User-Centred Validation and Calibration of Agent-Based Models. - Etienne Tack; Gilles Énée; Thomas Gaillard; Jean-Marie Fotsing; Frédéric Flouvat (ICAART (1), 2023)