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2020 – today
- 2023
[j47]Pierre Tufféry, Philippe Derreumaux:
A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution. Frontiers Bioinform. 3 (2023)- [j46]Florent Barbault
, Éric Brémond, Julien Rey, Pierre Tufféry, François Maurel:
DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion. J. Chem. Inf. Model. 63(16): 5220-5231 (2023) - [j45]Yasaman Karami, Samuel Murail, Julien Giribaldi, Benjamin Lefranc, Florian Defontaine, Olivier Lesouhaitier, Jérôme Leprince, Sjoerd Jacob de Vries, Pierre Tufféry:
Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. J. Chem. Inf. Model. 63(20): 6436-6450 (2023) - [j44]Julien Rey, Samuel Murail, Sjoerd Jacob de Vries, Philippe Derreumaux, Pierre Tufféry:
PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution. Nucleic Acids Res. 51(W1): 432-437 (2023) - 2021
- [j43]Chloé Quignot, Guillaume Postic, Hélène Bret, Julien Rey, Pierre Granger, Samuel Murail, Pablo Chacón, Jessica Andreani, Pierre Tufféry, Raphaël Guérois:
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. 49(Webserver-Issue): 277-284 (2021) - [j42]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:
Proteo3Dnet: a web server for the integration of structural information with interactomics data. Nucleic Acids Res. 49(Webserver-Issue): 567-572 (2021)
2010 – 2019
- 2019
- [j41]Julien Rey, Inès Rasolohery, Pierre Tufféry, Frédéric Guyon, Gautier Moroy:
PatchSearch: a web server for off-target protein identification. Nucleic Acids Res. 47(Webserver-Issue): W365-W372 (2019) - [j40]Yasaman Karami, Julien Rey, Guillaume Postic, Samuel Murail, Pierre Tufféry, Sjoerd Jacob de Vries:
DaReUS-Loop: a web server to model multiple loops in homology models. Nucleic Acids Res. 47(Webserver-Issue): W423-W428 (2019) - 2018
- [j39]Chloé Quignot, Julien Rey, Jinchao Yu, Pierre Tufféry, Raphaël Guérois, Jessica Andreani:
InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs. Nucleic Acids Res. 46(Webserver-Issue): W408-W416 (2018) - 2017
- [j38]Sjoerd Jacob de Vries, Julien Rey, Christina E. M. Schindler, Martin Zacharias, Pierre Tufféry:
The pepATTRACT web server for blind, large-scale peptide-protein docking. Nucleic Acids Res. 45(Webserver-Issue): W361-W364 (2017) - 2016
- [j37]Marie-Amandine Laurent, Dominique Bonnier, Nathalie Théret, Pierre Tufféry, Gautier Moroy:
In silico characterization of the interaction between LSKL peptide, a LAP-TGF-beta derived peptide, and ADAMTS1. Comput. Biol. Chem. 61: 155-161 (2016) - [j36]Alexis Lamiable, Pierre Thévenet, Pierre Tufféry:
A critical assessment of hidden markov model sub-optimal sampling strategies applied to the generation of peptide 3D models. J. Comput. Chem. 37(21): 2006-2016 (2016) - [j35]Alexis Lamiable, Pierre Thévenet, Julien Rey, Marek Vavrusa, Philippe Derreumaux, Pierre Tufféry:
PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Res. 44(Webserver-Issue): W449-W454 (2016) - [j34]Jinchao Yu, Marek Vavrusa, Jessica Andreani, Julien Rey, Pierre Tufféry, Raphaël Guérois:
InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information. Nucleic Acids Res. 44(Webserver-Issue): W542-W549 (2016) - 2015
- [j33]Jinchao Yu, Géraldine Picord, Pierre Tufféry, Raphaël Guérois:
HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling. Bioinform. 31(23): 3850-3852 (2015) - [j32]Frédéric Guyon, François Martz, Marek Vavrusa, Jérôme Bécot, Julien Rey, Pierre Tufféry:
BCSearch: fast structural fragment mining over large collections of protein structures. Nucleic Acids Res. 43(Webserver-Issue): W378-W382 (2015) - [j31]Céline M. Labbé, Julien Rey, David Lagorce, Marek Vavrusa, Jérôme Bécot, Olivier Sperandio, Bruno O. Villoutreix, Pierre Tufféry, Maria A. Miteva:
MTiOpenScreen: a web server for structure-based virtual screening. Nucleic Acids Res. 43(Webserver-Issue): W448-W454 (2015) - 2014
- [j30]Julien Rey, Patrick Deschavanne, Pierre Tufféry:
BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. Database J. Biol. Databases Curation 2014 (2014) - [j29]Julien Rey, Patrick Deschavanne, Pierre Tufféry:
BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. Database J. Biol. Databases Curation 2014 (2014) - [j28]Frédéric Guyon, Pierre Tufféry:
Fast protein fragment similarity scoring using a Binet-Cauchy kernel. Bioinform. 30(6): 784-791 (2014) - [j27]Adrien Saladin, Julien Rey, Pierre Thévenet, Martin Zacharias, Gautier Moroy, Pierre Tufféry:
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces. Nucleic Acids Res. 42(Webserver-Issue): 221-226 (2014) - [c5]Pierre Thévenet, Pierre Tufféry:
Exploring a Sub-optimal Hidden Markov Model Sampling Approach for De Novo Peptide Structure Modeling. BIOINFORMATICS 2014: 24-30 - 2012
- [j26]Pierre Thévenet, Yimin Shen, Julien Maupetit, Frédéric Guyon, Philippe Derreumaux, Pierre Tufféry:
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res. 40(Web-Server-Issue): 288-293 (2012) - 2011
- [j25]David Lagorce, Julien Maupetit, Jonathan B. Baell, Olivier Sperandio, Pierre Tufféry, Maria A. Miteva, Hervé Galons, Bruno O. Villoutreix:
The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections. Bioinform. 27(14): 2018-2020 (2011) - 2010
- [j24]Julien Maupetit, Philippe Derreumaux, Pierre Tufféry:
A fast method for large-scale De Novo peptide and miniprotein structure prediction. J. Comput. Chem. 31(4): 726-738 (2010) - [j23]Peter Schmidtke, Vincent Le Guilloux, Julien Maupetit, Pierre Tufféry:
fpocket: online tools for protein ensemble pocket detection and tracking. Nucleic Acids Res. 38(Web-Server-Issue): 582-589 (2010) - [j22]Maria A. Miteva, Frédéric Guyon, Pierre Tufféry:
Frog2: Efficient 3D conformation ensemble generator for small compounds. Nucleic Acids Res. 38(Web-Server-Issue): 622-627 (2010) - [c4]Hervé Ménager, Vivek Gopalan, Bertrand Néron, Sandrine Larroudé, Julien Maupetit, Adrien Saladin, Pierre Tufféry, Yentram Huyen, Bernard Caudron:
Bioinformatics Applications Discovery and Composition with the Mobyle Suite and MobyleNet. RED 2010: 11-22 - [c3]Edouard Strauser, Mikaël Naveau, Hervé Ménager, Julien Maupetit, Zoé Lacroix, Pierre Tufféry:
Semantic Map for Structural Bioinformatics: Enhanced Service Discovery Based on High Level Concept Ontology. RED 2010: 57-70
2000 – 2009
- 2009
- [j21]Bertrand Néron, Hervé Ménager, Corinne Maufrais, Nicolas Joly, Julien Maupetit, Sébastien Letort, Sébastien Carrère, Pierre Tufféry, Catherine Letondal:
Mobyle: a new full web bioinformatics framework. Bioinform. 25(22): 3005-3011 (2009) - [j20]Vincent Le Guilloux, Peter Schmidtke, Pierre Tufféry:
Fpocket: An open source platform for ligand pocket detection. BMC Bioinform. 10 (2009) - [j19]Flavien Quintus, Olivier Sperandio, Julien Grynberg, Michel Petitjean, Pierre Tufféry:
Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity. BMC Bioinform. 10 (2009) - [j18]Julien Maupetit, Philippe Derreumaux, Pierre Tufféry:
PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res. 37(Web-Server-Issue): 498-503 (2009) - [j17]Olivier Sperandio, Michel Petitjean, Pierre Tufféry:
wwLigCSRre: a 3D ligand-based server for hit identification and optimization. Nucleic Acids Res. 37(Web-Server-Issue): 504-509 (2009) - 2008
- [j16]Leslie Regad, Frédéric Guyon, Julien Maupetit, Pierre Tufféry, Anne-Claude Camproux:
A Hidden Markov Model applied to the protein 3D structure analysis. Comput. Stat. Data Anal. 52(6): 3198-3207 (2008) - 2007
- [j15]Ludovic Autin, Pierre Tufféry:
PMG: online generation of high-quality molecular pictures and storyboarded animations. Nucleic Acids Res. 35(Web-Server-Issue): 483-488 (2007) - [j14]T. Bohme Leite, D. Gomes, Maria A. Miteva, Jacques Chomilier, Bruno O. Villoutreix, Pierre Tufféry:
Frog: a FRee Online druG 3D conformation generator. Nucleic Acids Res. 35(Web-Server-Issue): 568-572 (2007) - [c2]Hervé Ménager, Zoé Lacroix, Pierre Tufféry:
Bioinformatics Services Discovery Using Ontology Classification. IEEE SCW 2007: 106-113 - 2006
- [j13]Julien Maupetit, R. Gautier, Pierre Tufféry:
SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace. Nucleic Acids Res. 34(Web-Server-Issue): 147-151 (2006) - [j12]Maria A. Miteva, Stephanie Violas, Matthieu Montès, David Gomez, Pierre Tufféry, Bruno O. Villoutreix:
FAF-Drugs: free ADME/tox filtering of compound collections. Nucleic Acids Res. 34(Web-Server-Issue): 738-744 (2006) - [c1]Pierre Tufféry, Zoé Lacroix, Hervé Ménager:
Semantic Map of Services for Structural Bioinformatics. SSDBM 2006: 217-224 - 2005
- [j11]Pierre Tufféry, Frédéric Guyon, Philippe Derreumaux:
Improved greedy algorithm for protein structure reconstruction. J. Comput. Chem. 26(5): 506-513 (2005) - [j10]C. Alland, F. Moreews, D. Boens, Mathilde Carpentier, S. Chiusa, Mathieu Lonquety, N. Renault, Y. Wong, Hubert Cantalloube, Jacques Chomilier, Joëlle Hochez, Joël Pothier, Bruno O. Villoutreix, Jean-François Zagury, Pierre Tufféry:
RPBS: a web resource for structural bioinformatics. Nucleic Acids Res. 33(Web-Server-Issue): 44-49 (2005) - [j9]Cédric Binisti, Ahmed Ali Salim, Pierre Tufféry:
PPG: online generation of protein pictures and animations. Nucleic Acids Res. 33(Web-Server-Issue): 320-323 (2005) - [j8]Maria A. Miteva, Pierre Tufféry, Bruno O. Villoutreix:
PCE: web tools to compute protein continuum electrostatics. Nucleic Acids Res. 33(Web-Server-Issue): 372-375 (2005) - 2004
- [j7]R. Gautier, Anne-Claude Camproux, Pierre Tufféry:
SCit: web tools for protein side chain conformation analysis. Nucleic Acids Res. 32(Web-Server-Issue): 508-511 (2004) - [j6]Frédéric Guyon, Anne-Claude Camproux, Joëlle Hochez, Pierre Tufféry:
SA-Search: a web tool for protein structure mining based on a Structural Alphabet. Nucleic Acids Res. 32(Web-Server-Issue): 545-548 (2004) - 2003
- [j5]R. Gautier, Pierre Tufféry:
Critical assessment of side-chain conformational space sampling procedures designed for quantifying the effect of side-chain environment. J. Comput. Chem. 24(15): 1950-1961 (2003) - 2002
- [j4]Pierre Tufféry:
CS-PSeq-Gen: Simulating the evolution of protein sequence under constraints. Bioinform. 18(7): 1015-1016 (2002)
1990 – 1999
- 1999
- [j3]Marie-Hélène Mucchielli-Giorgi, Serge A. Hazout, Pierre Tufféry:
PredAcc: prediction of solvent accessibility. Bioinform. 15(2): 176-177 (1999) - 1993
- [j2]Pierre Tufféry, Catherine Etchebest, Serge A. Hazout, Richard Lavery:
A critical comparison of search algorithms applied to the optimization of protein side-chain conformations. J. Comput. Chem. 14(7): 790-798 (1993)
1980 – 1989
- 1988
- [j1]Pierre Tufféry, Philippe Dessen, C. Mugnier, Serge A. Hazout:
Restriction map construction using a 'complete sentences compatibility' algorithm. Comput. Appl. Biosci. 4(1): 103-110 (1988)
Coauthor Index
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