Restriction map construction using a 'complete sentences compatibility' algorithm. - Pierre Tufféry; Philippe Dessen; C. Mugnier; Serge A. Hazout (Comput. Appl. Biosci., 1988)

A critical comparison of search algorithms applied to the optimization of protein side-chain conformations. - Pierre Tufféry; Catherine Etchebest; Serge A. Hazout; Richard Lavery (J. Comput. Chem., 1993)

PredAcc: prediction of solvent accessibility. - Marie-Hélène Mucchielli-Giorgi; Serge A. Hazout; Pierre Tufféry (Bioinform., 1999)

CS-PSeq-Gen: Simulating the evolution of protein sequence under constraints. - Pierre Tufféry (Bioinform., 2002)

Critical assessment of side-chain conformational space sampling procedures designed for quantifying the effect of side-chain environment. - R. Gautier; Pierre Tufféry (J. Comput. Chem., 2003)

SCit: web tools for protein side chain conformation analysis. - R. Gautier; Anne-Claude Camproux; Pierre Tufféry (Nucleic Acids Res., 2004)

SA-Search: a web tool for protein structure mining based on a Structural Alphabet. - Frédéric Guyon; Anne-Claude Camproux; Joëlle Hochez; Pierre Tufféry (Nucleic Acids Res., 2004)

Improved greedy algorithm for protein structure reconstruction. - Pierre Tufféry; Frédéric Guyon; Philippe Derreumaux (J. Comput. Chem., 2005)

RPBS: a web resource for structural bioinformatics. - C. Alland; François Moreews; D. Boens; Mathilde Carpentier; S. Chiusa; Mathieu Lonquety; N. Renault; Y. Wong; Hubert Cantalloube; Jacques Chomilier; Joëlle Hochez; Joël Pothier; et al. (Nucleic Acids Res., 2005)

PPG: online generation of protein pictures and animations. - Cédric Binisti; Ahmed Ali Salim; Pierre Tufféry (Nucleic Acids Res., 2005)

PCE: web tools to compute protein continuum electrostatics. - Maria A. Miteva; Pierre Tufféry; Bruno O. Villoutreix (Nucleic Acids Res., 2005)

Semantic Map of Services for Structural Bioinformatics. - Pierre Tufféry; Zoé Lacroix; Hervé Ménager (SSDBM, 2006)

SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace. - Julien Maupetit; R. Gautier; Pierre Tufféry (Nucleic Acids Res., 2006)

FAF-Drugs: free ADME/tox filtering of compound collections. - Maria A. Miteva; Stephanie Violas; Matthieu Montès; David Gomez; Pierre Tufféry; Bruno O. Villoutreix (Nucleic Acids Res., 2006)

Bioinformatics Services Discovery Using Ontology Classification. - Hervé Ménager; Zoé Lacroix; Pierre Tufféry (IEEE SCW, 2007)

PMG: online generation of high-quality molecular pictures and storyboarded animations. - Ludovic Autin; Pierre Tufféry (Nucleic Acids Res., 2007)

Frog: a FRee Online druG 3D conformation generator. - T. Bohme Leite; D. Gomes; Maria A. Miteva; Jacques Chomilier; Bruno O. Villoutreix; Pierre Tufféry (Nucleic Acids Res., 2007)

A Hidden Markov Model applied to the protein 3D structure analysis. - Leslie Regad; Frédéric Guyon; Julien Maupetit; Pierre Tufféry; Anne-Claude Camproux (Comput. Stat. Data Anal., 2008)

Mobyle: a new full web bioinformatics framework. - Bertrand Néron; Hervé Ménager; Corinne Maufrais; Nicolas Joly; Julien Maupetit; Sébastien Letort; Sébastien Carrère; Pierre Tufféry; Catherine Letondal (Bioinform., 2009)

Fpocket: An open source platform for ligand pocket detection. - Vincent Le Guilloux; Peter Schmidtke; Pierre Tufféry (BMC Bioinform., 2009)

Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity. - Flavien Quintus; Olivier Sperandio; Julien Grynberg; Michel Petitjean; Pierre Tufféry (BMC Bioinform., 2009)

PEP-FOLD: an online resource for de novo peptide structure prediction. - Julien Maupetit; Philippe Derreumaux; Pierre Tufféry (Nucleic Acids Res., 2009)

wwLigCSRre: a 3D ligand-based server for hit identification and optimization. - Olivier Sperandio; Michel Petitjean; Pierre Tufféry (Nucleic Acids Res., 2009)

Bioinformatics Applications Discovery and Composition with the Mobyle Suite and MobyleNet. - Hervé Ménager; Vivek Gopalan; Bertrand Néron; Sandrine Larroudé; Julien Maupetit; Adrien Saladin; Pierre Tufféry; Yentram Huyen; Bernard Caudron (RED, 2010)

Semantic Map for Structural Bioinformatics: Enhanced Service Discovery Based on High Level Concept Ontology. - Edouard Strauser; Mikaël Naveau; Hervé Ménager; Julien Maupetit; Zoé Lacroix; Pierre Tufféry (RED, 2010)

A fast method for large-scale De Novo peptide and miniprotein structure prediction. - Julien Maupetit; Philippe Derreumaux; Pierre Tufféry (J. Comput. Chem., 2010)

Frog2: Efficient 3D conformation ensemble generator for small compounds. - Maria A. Miteva; Frédéric Guyon; Pierre Tufféry (Nucleic Acids Res., 2010)

fpocket: online tools for protein ensemble pocket detection and tracking. - Peter Schmidtke; Vincent Le Guilloux; Julien Maupetit; Pierre Tufféry (Nucleic Acids Res., 2010)

The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections. - David Lagorce; Julien Maupetit; Jonathan B. Baell; Olivier Sperandio; Pierre Tufféry; Maria A. Miteva; Hervé Galons; Bruno O. Villoutreix (Bioinform., 2011)

PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. - Pierre Thévenet; Yimin Shen; Julien Maupetit; Frédéric Guyon; Philippe Derreumaux; Pierre Tufféry (Nucleic Acids Res., 2012)

Exploring a Sub-optimal Hidden Markov Model Sampling Approach for De Novo Peptide Structure Modeling. - Pierre Thévenet; Pierre Tufféry (BIOINFORMATICS, 2014)

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)

Fast protein fragment similarity scoring using a Binet-Cauchy kernel. - Frédéric Guyon; Pierre Tufféry (Bioinform., 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)

HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling. - Jinchao Yu; Géraldine Picord; Pierre Tufféry; Raphaël Guérois (Bioinform., 2015)

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)

In silico characterization of the interaction between LSKL peptide, a LAP-TGF-beta derived peptide, and ADAMTS1. - Marie-Amandine Laurent; Dominique Bonnier; Nathalie Théret; Pierre Tufféry; Gautier Moroy (Comput. Biol. Chem., 2016)

A critical assessment of hidden markov model sub-optimal sampling strategies applied to the generation of peptide 3D models. - Alexis Lamiable; Pierre Thévenet; Pierre Tufféry (J. Comput. Chem., 2016)

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)

A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution. - Pierre Tufféry; Philippe Derreumaux (Frontiers Bioinform., 2023)

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)

Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. - Yasaman Karami; Samuel Murail; Julien Giribaldi; Benjamin Lefranc; Florian Defontaine; Olivier Lesouhaitier; Jérôme Leprince; Sjoerd Jacob de Vries; Pierre Tufféry (J. Chem. Inf. Model., 2023)