sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank. - Esther Kellenberger; Pascal Muller; Claire Schalon; Guillaume Bret; Nicolas Foata; Didier Rognan (J. Chem. Inf. Model., 2006)

Assessing the Scaffold Diversity of Screening Libraries. - Mireille Krier; Guillaume Bret; Didier Rognan (J. Chem. Inf. Model., 2006)

IChemPIC: A Random Forest Classifier of Biological and Crystallographic Protein-Protein Interfaces. - Franck Da Silva; Jérémy Desaphy; Guillaume Bret; Didier Rognan (J. Chem. Inf. Model., 2015)

sc-PDB: a 3D-database of ligandable binding sites - 10 years on. - Jérémy Desaphy; Guillaume Bret; Didier Rognan; Esther Kellenberger (Nucleic Acids Res., 2015)

Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015. - Inna Slynko; Franck Da Silva; Guillaume Bret; Didier Rognan (J. Comput. Aided Mol. Des., 2016)

Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2. - Priscila da Silva Figueiredo Celestino Gomes; Franck Da Silva; Guillaume Bret; Didier Rognan (J. Comput. Aided Mol. Des., 2018)

All in One: Cavity Detection, Druggability Estimate, Cavity-Based Pharmacophore Perception, and Virtual Screening. - Viet-Khoa Tran-Nguyen; Franck Da Silva; Guillaume Bret; Didier Rognan (J. Chem. Inf. Model., 2019)

True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better. - Viet-Khoa Tran-Nguyen; Guillaume Bret; Didier Rognan (J. Chem. Inf. Model., 2021)

Comparing transmembrane protein structures with ATOLL. - Célien Jacquemard; Guillaume Bret; Thomas Grutter; Esther Kellenberger (Bioinform., 2022)

Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2. - Merveille K. I. Eguida; Guillaume Bret; François Sindt; Fengling Li; Irene Chau; Suzanne Ackloo; Cheryl H. Arrowsmith; Albina Bolotokova; Pegah Ghiabi; Elisa Gibson; Levon Halabelian; Scott Houliston; et al. (J. Chem. Inf. Model., 2024)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - Fengling Li; Suzanne Ackloo; Cheryl H. Arrowsmith; Fuqiang Ban; Christopher J. Barden; Hartmut Beck; Jan Beránek; Francois Berenger; Albina Bolotokova; Guillaume Bret; Marko Breznik; Emanuele Carosati; et al. (J. Chem. Inf. Model., 2024)

Benchmarking AlphaFold-Generated Structures of Chemokine-Chemokine Receptor Complexes. - Lauri Urvas; Luca Chiesa; Guillaume Bret; Célien Jacquemard; Esther Kellenberger (J. Chem. Inf. Model., 2024)

On the Difficulty to Rescore Hits from Ultralarge Docking Screens. - François Sindt; Guillaume Bret; Didier Rognan (J. Chem. Inf. Model., 2025)