Unrolr: Structural analysis of protein conformations using stochastic proximity embedding. - Jérôme Eberhardt; Roland H. Stote; Annick Dejaegere (J. Comput. Chem., 2018)

Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. - Lea El-Khoury; Diogo Santos-Martins; Sukanya Sasmal; Jérôme Eberhardt; Giulia Bianco; Francesca Alessandra Ambrosio; Leonardo Solis-Vasquez; Andreas Koch 001; Stefano Forli; David L. Mobley (J. Comput. Aided Mol. Des., 2019)

D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU. - Diogo Santos-Martins; Jérôme Eberhardt; Giulia Bianco; Leonardo Solis-Vasquez; Francesca Alessandra Ambrosio; Andreas Koch 001; Stefano Forli (J. Comput. Aided Mol. Des., 2019)

Parallelizing Irregular Computations for Molecular Docking. - Leonardo Solis-Vasquez; Diogo Santos-Martins; Andreas F. Tillack; Andreas Koch 001; Jérôme Eberhardt; Stefano Forli (IA3@SC, 2020)

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. - Jérôme Eberhardt; Diogo Santos-Martins; Andreas F. Tillack; Stefano Forli (J. Chem. Inf. Model., 2021)

CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis. - Niccolò Bruciaferri; Jérôme Eberhardt; Manuel A. Llanos; Johannes R. Loeffler; Matthew Holcomb; Monica L. Fernández-Quintero; Diogo Santos-Martins; Andrew B. Ward; Stefano Forli (J. Chem. Inf. Model., 2024)