BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. - Julien Rey; Patrick Deschavanne; Pierre Tufféry (Database J. Biol. Databases Curation, 2014)

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces. - Adrien Saladin; Julien Rey; Pierre Thévenet; Martin Zacharias; Gautier Moroy; Pierre Tufféry (Nucleic Acids Res., 2014)

BCSearch: fast structural fragment mining over large collections of protein structures. - Frédéric Guyon; François Martz; Marek Vavrusa; Jérôme Bécot; Julien Rey; Pierre Tufféry (Nucleic Acids Res., 2015)

MTiOpenScreen: a web server for structure-based virtual screening. - Céline M. Labbé; Julien Rey; David Lagorce; Marek Vavrusa; Jérôme Bécot; Olivier Sperandio; Bruno O. Villoutreix; Pierre Tufféry; Maria A. Miteva (Nucleic Acids Res., 2015)

PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex. - Alexis Lamiable; Pierre Thévenet; Julien Rey; Marek Vavrusa; Philippe Derreumaux; Pierre Tufféry (Nucleic Acids Res., 2016)

InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information. - Jinchao Yu; Marek Vavrusa; Jessica Andreani; Julien Rey; Pierre Tufféry; Raphaël Guérois (Nucleic Acids Res., 2016)

The pepATTRACT web server for blind, large-scale peptide-protein docking. - Sjoerd Jacob de Vries; Julien Rey; Christina E. M. Schindler; Martin Zacharias; Pierre Tufféry (Nucleic Acids Res., 2017)

InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs. - Chloé Quignot; Julien Rey; Jinchao Yu; Pierre Tufféry; Raphaël Guérois; Jessica Andreani (Nucleic Acids Res., 2018)

DaReUS-Loop: a web server to model multiple loops in homology models. - Yasaman Karami; Julien Rey; Guillaume Postic; Samuel Murail; Pierre Tufféry; Sjoerd Jacob de Vries (Nucleic Acids Res., 2019)

PatchSearch: a web server for off-target protein identification. - Julien Rey; Inès Rasolohery; Pierre Tufféry; Frédéric Guyon; Gautier Moroy (Nucleic Acids Res., 2019)

Proteo3Dnet: a web server for the integration of structural information with interactomics data. - Guillaume Postic; Jessica Andreani; Julien Marcoux; Victor Reys; Raphaël Guérois; Julien Rey; Emmanuelle Mouton-Barbosa; Yves Vandenbrouck; Sarah Cianférani; Odile Burlet-Schiltz; Gilles Labesse; Pierre Tufféry (Nucleic Acids Res., 2021)

InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps. - Chloé Quignot; Guillaume Postic; Hélène Bret; Julien Rey; Pierre Granger; Samuel Murail; Pablo Chacón; Jessica Andreani; Pierre Tufféry; Raphaël Guérois (Nucleic Acids Res., 2021)

PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution. - Julien Rey; Samuel Murail; Sjoerd Jacob de Vries; Philippe Derreumaux; Pierre Tufféry (Nucleic Acids Res., 2023)

DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion. - Florent Barbault; Éric Brémond; Julien Rey; Pierre Tufféry; François Maurel (J. Chem. Inf. Model., 2023)