P. Tufféry

发表

A new approach to the rapid determination of protein side chain conformations.

R. Lavery, C. Etchebest, P. Tufféry, 1991, Journal of biomolecular structure & dynamics.

Assessing 3D scores for protein structure fragment mining

Pierre Tufféry, Frédéric Guyon, F. Guyon, 2010 .

An information gain-based approach for evaluating protein structure models

P. Tufféry, N. Janel, G. Moroy, 2020, Computational and Structural Biotechnology Journal.

A coarse‐grained protein force field for folding and structure prediction

P. Derreumaux, P. Tufféry, Julien Maupetit, 2007, Proteins.

Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction.

P. Derreumaux, P. Tufféry, Julien Maupetit, 2014, Journal of chemical theory and computation.

The CH1α domain of mucosal gp41 IgA contributes to antibody specificity and antiviral functions in HIV-1 highly exposed Sero-Negative individuals

P. Tufféry, M. Bomsel, Tahar Bouceba, 2020, PLoS pathogens.

PatchSearch: a web server for off-target protein identification

F. Guyon, P. Tufféry, G. Moroy, 2019, Nucleic Acids Res..

Enhanced protein fold recognition using a structural alphabet

P. Deschavanne, P. Tufféry, 2009, Proteins.

Predicting the disulfide bonding state of cysteines using protein descriptors

P Tufféry, S Hazout, P. Tufféry, 2002, Proteins.

Interfering peptides targeting protein-protein interactions: the next generation of drugs?

P. Tufféry, A. Rebollo, N. Wolff, 2017, Drug discovery today.

A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major

P. Derreumaux, P. Tufféry, N. Carels, 2017, Bioinformatics and biology insights.

Packing and recognition of protein structural elements: A new approach applied to the 4‐helix bundle of myohemerythrin

Pierre Tufféry, Richard Lavery, R. Lavery, 1993, Proteins.

DaReUS-Loop: a web server to model multiple loops in homology models

P. Tufféry, Yasaman Karami, Guillaume Postic, 2019, Nucleic Acids Res..

Discretization of 3 D protein conformations by learning fragments library and their short range dependence using a Hidden Markov Model

A. Camproux, P. Tufféry, R. Gautier, 2003 .

A Hidden Markov Model applied to the analysis of protein 3 D-structures

P. Tufféry, F. Guyon, F. Guyon, 2005 .

Missense mutations in SLC26A8, encoding a sperm-specific activator of CFTR, are associated with human asthenozoospermia.

P. Tufféry, P. Ray, T. Dirami, 2013, American journal of human genetics.

Databases and ontologies Mobyle : a new full web bioinformatics framework

P. Tufféry, C. Letondal, S. Carrère, 2009 .

PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions?

P. Tufféry, A. Rebollo, Louise Fliedel, 2022, Biomolecules.

SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking

P. Tufféry, S. D. de Vries, G. Moroy, 2021, Frontiers in Molecular Biosciences.

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.

Marc Baaden, Samuela Pasquali, Maria Kalimeri, 2014, Chemical Society reviews.

Modelling of transmembrane α-helix bundles

R. Lavery, C. Etchebest, P. Tufféry, 1995 .

Steps Towards Predicting the Structure of Membrane Proteins

R. Lavery, C. Etchebest, P. Tufféry, 1994 .

In silico structural characterization of protein targets for drug development against Trypanosoma cruzi

P. Derreumaux, P. Tufféry, N. Carels, 2016, Journal of Molecular Modeling.

Relative Local Convexity Approaches for Accessibility Studies of Molecular Regions

P. Mezey, P. Tufféry, S. Hazout, 1998 .

Peptide-Based Strategies Against SARS-CoV-2 Attack: An Updated In Silico Perspective

P. Tufféry, G. Moroy, 2022, Frontiers in Drug Discovery.

Candidate Fragments Prediction and their Assembly with a Greedy Algorithm and a Coarse-Grained Force Field to solve Protein Folding

F. Guyon, P. Derreumaux, A. Camproux, 2007 .

Binding and Kinetic Analysis of Human Protein Phosphatase PP2A Interactions with Caspase 9 Protein and the Interfering Peptide C9h

P. Tufféry, J. Bravo, A. Rebollo, 2022, Pharmaceutics.

Lys53 of Ribosomal Protein L36AL and the CCA End of a tRNA at the P/E Hybrid Site Are in Close Proximity on the Human Ribosome

P. Tufféry, K. Nierhaus, C. Hountondji, 2012, Chembiochem : a European journal of chemical biology.

fpocket: online tools for protein ensemble pocket detection and tracking

Vincent Le Guilloux, Pierre Tufféry, Julien Maupetit, 2010, Nucleic Acids Res..

Progress with peptide scanning to study structure-activity relationships: the implications for drug discovery

P. Tufféry, J. Leprince, Stéphanie Eustache, 2016, Expert opinion on drug discovery.

Head-to-tail peptide cyclization: new directions and application to urotensin II and Nrf2

O. Lesouhaitier, P. Tufféry, Yasaman Karami, 2022, bioRxiv.

Frog2: Efficient 3D conformation ensemble generator for small compounds

Pierre Tufféry, Maria A. Miteva, Frédéric Guyon, 2010, Nucleic Acids Res..

PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex

Pierre Tufféry, Julien Rey, Marek Vavrusa, 2016, Nucleic Acids Res..

The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections

Pierre Tufféry, Olivier Sperandio, David Lagorce, 2011, Bioinform..

Fpocket: An open source platform for ligand pocket detection

Vincent Le Guilloux, Pierre Tufféry, Peter Schmidtke, 2009, BMC Bioinformatics.

A model for the photosystem II reaction center core including the structure of the primary donor P680.

P Tuffery, C Etchebest, C. Etchebest, 1996, Biochemistry.

MTiOpenScreen: a web server for structure-based virtual screening

Pierre Tufféry, Olivier Sperandio, Céline M. Labbé, 2015, Nucleic Acids Res..

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

Pierre Tufféry, Julien Rey, Pierre Thévenet, 2014, Nucleic Acids Res..

Fast protein fragment similarity scoring using a Binet-Cauchy kernel

Pierre Tufféry, Frédéric Guyon, F. Guyon, 2014, Bioinform..

BIOINFORMATICS ORIGINAL PAPER

Pierre Tufféry, Sébastien Carrère, Catherine Letondal, 2022 .

Critical assessment of side‐chain conformational space sampling procedures designed for quantifying the effect of side‐chain environment

P. Tufféry, R. Gautier, P. Tufféry, 2003, J. Comput. Chem..

Bi-Functional Peptides as a New Therapeutic Tool for Hepatocellular Carcinoma

P. Tufféry, A. Rebollo, T. Teesalu, 2021, Pharmaceutics.

Pepscan Approach for the Identification of Protein–Protein Interfaces: Lessons from Experiment

P. Tufféry, A. Rebollo, E. Savier, 2021, Biomolecules.

PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides

Pierre Tufféry, Pierre Thévenet, Frédéric Guyon, 2012, Nucleic Acids Res..

A fast method for large‐scale De Novo peptide and miniprotein structure prediction

Pierre Tufféry, Julien Maupetit, Philippe Derreumaux, 2009, J. Comput. Chem..

DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins

F. Guyon, P. Tufféry, Yasaman Karami, 2018, Scientific Reports.

A Generalized Attraction-Repulsion Potential and Revisited Fragment Library Improves PEP-FOLD Peptide Structure Prediction.

N. Mousseau, P. Tufféry, Vincent Binette, 2022, Journal of chemical theory and computation.

Proteo3Dnet: a web server for the integration of structural information with interactomics data

G. Labesse, R. Guérois, P. Tufféry, 2021, Nucleic Acids Res..

A Functional Role for the Monomethylated Gln-51 and Lys-53 Residues of the 49GGQTK53 Motif of eL42 from Human 80S Ribosomes

P. Tufféry, Tahar Bouceba, J. Nakayama, 2017, The open biochemistry journal.

The CCA-end of P-tRNA Contacts Both the Human RPL36AL and the A-site Bound Translation Termination Factor eRF1 at the Peptidyl Transferase Center of the Human 80S Ribosome

P. Tufféry, L. Frolova, K. Nierhaus, 2014, The open biochemistry journal.

Cloning and modeling of CD8 beta in the amphibian ambystoma Mexicanum. Evolutionary conserved structures for interactions with major histocompatibility complex (MHC) class I molecules.

C. Etchebest, P. Tufféry, F. Guillet, 2002, Gene.

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

P. Chacón, R. Guérois, P. Tufféry, 2021, Nucleic Acids Res..

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Arne Elofsson, Matthias Rarey, Anastassis Perrakis, 2020, F1000Research.

Coarse‐grained and atomic resolution biomolecular docking with the ATTRACT approach

Martin Zacharias, Samuel Murail, Pierre Tuffery, 2019, Proteins.

A triple-mutated allele of granzyme B incapable of inducing apoptosis

A. Samri, B. Autran, P. Debré, 2003, Proceedings of the National Academy of Sciences of the United States of America.

PCE: web tools to compute protein continuum electrostatics

Pierre Tufféry, Bruno O. Villoutreix, Maria A. Miteva, 2005, Nucleic Acids Res..

BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes

Pierre Tufféry, Julien Rey, Patrick Deschavanne, 2014, Database J. Biol. Databases Curation.

Frog: a FRee Online druG 3D conformation generator

Jacques Chomilier, Pierre Tufféry, Bruno O. Villoutreix, 2007, Nucleic Acids Res..

Hidden Markov model approach for identifying the modular framework of the protein backbone.

J F Boisvieux, A C Camproux, P Tuffery, 1999, Protein engineering.

Evolutionary conserved protein motifs drive attachment of the plant nucleoskeleton at nuclear pores

P. Tufféry, A. Probst, C. Tatout, 2021, bioRxiv.

PEP-FOLD: an online resource for de novo peptide structure prediction

Pierre Tufféry, Julien Maupetit, Philippe Derreumaux, 2009, Nucleic Acids Res..

Prediction of protein side chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space.

P Tufféry, S Hazout, C Etchebest, 1997, Protein engineering.

Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study.

P Tuffery, C Etchebest, R Lavery, 1994, Journal of molecular biology.

aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species

E. Denamur, P. Tufféry, O. Clermont, 2009, BMC Microbiology.

HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling

Pierre Tufféry, Raphaël Guérois, Jinchao Yu, 2015, Bioinform..

In silico characterization of the interaction between LSKL peptide, a LAP-TGF-beta derived peptide, and ADAMTS1

Pierre Tufféry, Nathalie Théret, Gautier Moroy, 2016, Comput. Biol. Chem..

Protease profiling of liver fibrosis reveals the ADAM metallopeptidase with thrombospondin type 1 motif, 1 as a central activator of transforming growth factor beta

P. Tufféry, B. Mari, G. Baffet, 2011, Hepatology.

SA-Search: a web tool for protein structure mining based on a Structural Alphabet

Pierre Tufféry, Anne-Claude Camproux, Frédéric Guyon, 2004, Nucleic Acids Res..

Detecting Protein Candidate Fragments Using a Structural Alphabet Profile Comparison Approach

Frédéric Guyon, Pierre Tuffery, Géraldine Picord, 2013, PloS one.

Improved greedy algorithm for protein structure reconstruction

Pierre Tufféry, Frédéric Guyon, Philippe Derreumaux, 2005, J. Comput. Chem..

A hidden markov model derived structural alphabet for proteins.

A C Camproux, R Gautier, P Tufféry, 2004, Journal of molecular biology.

Exploring the use of a structural alphabet for structural prediction of protein loops

Pierre Tufféry, A. C. Camproux, A. G. Brevern, 2001 .

Analyzing patterns between regular secondary structures using short structural building blocks defined by a hidden Markov model

Pierre Tufféry, Cécile André, Serge Hazout, 1999 .

Protein structural alphabets: beyond the secondary structure description

Pierre Tufféry, Anne-Claude Camproux, Alexandre G. de Brevern, 2001 .

De novo peptide structure prediction: an overview.

Julien Rey, Pierre Thévenet, Gautier Moroy, 2015, Methods in molecular biology.

Exploring a Sub-optimal Hidden Markov Model Sampling Approach for De Novo Peptide Structure Modeling

Pierre Tufféry, Pierre Thévenet, P. Tufféry, 2014, BIOINFORMATICS.

A Hidden Markov Model applied to the protein 3D structure analysis

Pierre Tufféry, Anne-Claude Camproux, Leslie Regad, 2008, Comput. Stat. Data Anal..

Hidden Markov model-derived structural alphabet for proteins: the learning of protein local shapes captures sequence specificity.

A C Camproux, P Tufféry, A. Camproux, 2005, Biochimica et biophysica acta.

RPBS: a web resource for structural bioinformatics

Jacques Chomilier, Pierre Tufféry, Bruno O. Villoutreix, 2005, Nucleic Acids Res..

XmMol: an X11 and motif program for macromolecular visualization and modeling.

P Tufféry, P. Tufféry, 1995, Journal of molecular graphics.

FAF-Drugs: free ADME/tox filtering of compound collections

Pierre Tufféry, Bruno O. Villoutreix, Maria A. Miteva, 2006, Nucleic Acids Res..

Isotype modulates epitope specificity, affinity, and antiviral activities of anti–HIV-1 human broadly neutralizing 2F5 antibody

L. Lopalco, P. Tufféry, M. Bomsel, 2012, Proceedings of the National Academy of Sciences.

InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information

Pierre Tufféry, Julien Rey, Marek Vavrusa, 2016, Nucleic Acids Res..

Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets

Pierre Tufféry, Julien Rey, Bruno O. Villoutreix, 2018, Oncotarget.

Probing protein interaction networks by combining MS-based proteomics and structural data integration.

Odile Burlet-Schiltz, Raphael Guerois, Guillaume Postic, 2020, Journal of proteome research.

A novel computational method for head-to-tail peptide cyclization: application to urotensin II

P. Tufféry, Yasaman Karami, S. D. de Vries, 2022 .

A critical comparison of search algorithms applied to the optimization of protein side‐chain conformations

Pierre Tufféry, Serge A. Hazout, Catherine Etchebest, 1993, J. Comput. Chem..

Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches

Philippe Derreumaux, Pierre Tuffery, P. Derreumaux, 2012, Journal of The Royal Society Interface.

Probing the quality control mechanism of the Escherichia coli twin-arginine translocase with folding variants of a de novo–designed heme protein

P. Derreumaux, P. Tufféry, P. Dutton, 2018, The Journal of Biological Chemistry.

A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution

P. Derreumaux, P. Tufféry, 2022, bioRxiv.

PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution

P. Derreumaux, P. Tufféry, S. D. de Vries, 2023, Nucleic Acids Res..

SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace

Pierre Tufféry, Julien Maupetit, R. Gautier, 2006, Nucleic Acids Res..

The pepATTRACT web server for blind, large-scale peptide–protein docking

Pierre Tufféry, Julien Rey, Sjoerd J. de Vries, 2017, Nucleic Acids Res..

Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity

Pierre Tufféry, Olivier Sperandio, Michel Petitjean, 2009, BMC Bioinformatics.

InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs

Pierre Tufféry, Julien Rey, Jessica Andreani, 2018, Nucleic Acids Res..

In Silico and In Vivo Studies of a Tumor-Penetrating and Interfering Peptide with Antitumoral Effect on Xenograft Models of Breast Cancer

P. Tufféry, A. Rebollo, S. Loisel, 2023, Pharmaceutics.

Isolation of Primary Hepatocytes for Testing Tumor Penetrating Peptides.

P. Tufféry, A. Rebollo, H. Bruzzoni-Giovanelli, 2021, Methods in molecular biology.

The search of sequence variants using a constrained protein evolution simulation approach

Pierre Tufféry, Sjoerd de Vries, P. Tufféry, 2020, Computational and structural biotechnology journal.

PredAcc: prediction of solvent accessibility

Pierre Tufféry, Serge A. Hazout, Marie-Hélène Mucchielli-Giorgi, 1999, Bioinform..

Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations.

P. Derreumaux, P. Tufféry, P. Nguyen, 2022, Methods in molecular biology.

Identification of peptides interfering with the LRRK2/PP1 interaction

P. Tufféry, A. Rebollo, H. Bruzzoni-Giovanelli, 2020, PloS one.

Identification of peptides interfering the lrrk2/pp1 interaction

P. Tufféry, A. Rebollo, C. Dong, 2019, bioRxiv.

Accessing external innovation in drug discovery and development

Pierre Tufféry, P. Tufféry, 2015, Expert opinion on drug discovery.

to record in KAR

P. Tufféry, P. Dutton, F. Sterpone, 2022 .

PMG: online generation of high-quality molecular pictures and storyboarded animations

Pierre Tufféry, Ludovic Autin, P. Tufféry, 2007, Nucleic Acids Res..

A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments

Maria A Miteva, Bruno O Villoutreix, Tania Pencheva, 2019, International journal of molecular sciences.

CS-PSeq-Gen: Simulating the evolution of protein sequence under constraints

P. Tufféry, P. Tufféry, 2002, Bioinform..

DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion

P. Tufféry, É. Brémond, Julien Rey, 2023, J. Chem. Inf. Model..

DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins

Yasaman Karami, Pierre Tufféry, Frédéric Guyon, 2018, Scientific Reports.

BCSearch: fast structural fragment mining over large collections of protein structures

Pierre Tufféry, Julien Rey, Marek Vavrusa, 2015, Nucleic Acids Res..

Bmc Microbiology

E. Denamur, P. Tufféry, O. Clermont, 2022 .

Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm

Philippe Derreumaux, Pierre Tuffery, P. Derreumaux, 2005, Proteins.

SCit: web tools for protein side chain conformation analysis

Pierre Tufféry, Anne-Claude Camproux, R. Gautier, 2004, Nucleic Acids Res..

wwLigCSRre: a 3D ligand-based server for hit identification and optimization

Pierre Tufféry, Olivier Sperandio, Michel Petitjean, 2009, Nucleic Acids Res..

Frog: a FRee Online druG 3D conformation generator

P. Tufféry, B. Villoutreix, M. Miteva, 2007, Nucleic Acids Res..