2023

Barbault F, Brémond E, Rey J, Tufféry P, Maurel F.
DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion.
J Chem Inf Model. 2023 Aug 28;63(16):5220-5231.

Rey J, Murail S, de Vries SJ, Derreumaux P, Tuffery P.
PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution.
Nucleic Acids Res. 2023 Jul 5;51(W1):W432-W437.

2021

Murail S, de Vries SJ, Rey J, Moroy G, Tuffery P.
SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking.
Front Mol Biosci. 2021 Sep 17;8:716466.

Quignot C, Postic G, Bret H, Rey J, Granger P, Murail S, Chacón P, Andreani J, Tufféry P, Guerois R.
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.
Nucleic Acids Res. 2021 Jul 2;49(W1):W277-W284.

Postic G, Andreani J, Marcoux J, Reys V, Guerois R, Rey J, Mouton-Barbosa E, Vandenbrouck Y, Cianferani S, Burlet-Schiltz O, Labesse G, Tufféry P.
Proteo3Dnet: a web server for the integration of structural information with interactomics data
Nucleic Acids Res. 2021 Jul 2;49(W1):W567-W572.

2019

Lagarde N, Goldwaser E, Pencheva T, Jereva D, Pajeva I, Rey J, Tuffery P, Villoutreix BO, Miteva MA.
A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments.
Int J Mol Sci. 2019 Sep 19;20(18):4648.

Rey J, Rasolohery I, Tufféry P, Guyon F, Moroy G.
PatchSearch: a web server for off-target protein identification.
Nucleic Acids Res. 2019 Jul 2;47(W1):W365-W372.

Karami Y, Rey J, Postic G, Murail S, Tufféry P, de Vries SJ.
DaReUS-Loop: a web server to model multiple loops in homology models.
Nucleic Acids Res. 2019 Jul 2;47(W1):W423-W428.

Stratmann D, Pathmanathan JS, Postic G, Rey J, Chomilier J.
TEF 2.0: a graph-based method for decomposing protein structures into closed loops.
J Biomol Struct Dyn. 2019 Oct;37(16):4140-4150.

2018

Quignot C, Rey J, Yu J, Tufféry P, Guerois R, Andreani J.
InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs.
Nucleic Acids Res. 2018 Jul 2;46(W1):W408-W416.

2017

De Vries SJ, Rey J, Schindler CEM, Zacharias M, Tuffery P.
The pepATTRACT web server for blind, large-scale peptide-protein docking.
Nucleic Acids Res. 2017 Apr 29.

2016

Lamiable A, Thévenet P, Rey J, Vavrusa M, Derreumaux P, Tufféry P.
PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex.
Nucleic Acids Res. 2016 Jul 8;44(W1):W449-54.

Yu J, Vavrusa M, Andreani J, Rey J, Tufféry P, Guerois R.
InterEvDock: A docking server to predict the structure of protein-protein interactions using evolutionary information.
Nucleic Acids Res. 2016 Jul 8;44(W1):W542-9.

2015

Yu J, Picord G, Tufféry P, Guerois R.
HHalign-KBest: exploring sub-optimal alignments for remote homology comparative modeling
Bioinformatics. 2015 Dec 1;31(23):3850-2.

Labbé C, Rey J, Lagorce D, Vavruša M, Becot J, Sperandio O, Villoutreix B, Tufféry P, Miteva M.
MTiOpenScreen: a web server for structure-based virtual screening.
Nucleic Acids Res. 2015 Jul 1;43(W1):W448-54.

Guyon F, Martz F, Vavruša M, Bécot J, Rey J, Tufféry P.
BCSearch: fast structural fragment mining over large collections of protein structures.
Nucleic Acids Res. 2015 Jul 1;43(W1):W378-82.

2014

Rey J, Deschavanne P, Tufféry P.
BactPepDB: a database of predicted peptides from an exhaustive survey of complete prokaryote genomes.
Database (Oxford). 2014 Nov 6;2014. Print 2014.

Saladin A, Rey J, Thévenet P, Zacharias M, Moroy G, Tufféry P.
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W221-6.

Shen Y, Maupetit J, Derreumaux P, Tufféry P.
Improved PEP-FOLD approach for peptide and miniprotein structure prediction
J. Chem. Theor. Comput. 2014; 10:4745-4758

Guyon F, Tufféry P.
Fast protein fragment similarity scoring using a Binet-Cauchy kernel.
Bioinformatics. 2014 Mar 15;30(6):784-91.

2013

Shen Y, Picord G, Guyon F, Tuffery P.
Detecting protein candidate fragments using a structural alphabet profile comparison approach.
PLoS One. 2013 Nov 26;8(11).

2012

Thévenet P, Shen Y, Maupetit J, Guyon F, Derreumaux P, Tufféry P.
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W288-93.