Liste des publications

2024

• @TOME 3.0: Interfacing Protein Structure Modeling and Ligand Docking

  Pons JL, Reys V, Grand F, Moreau V, Gracy J, Exner TE, Labesse G, J Mol Biol, 2024

• The structural landscape and diversity of Pyricularia oryzae MAX effectors revisited

  Lahfa M, Barthe P, deGuillen K, Cesari S, Raji M, Kroj T, Le Naour-Vernet M, Hoh F, Gladieux P, Roumestand C, Gracy J, Declerck N, Padilla A, PLoS Pathog, 2024

2023

• Adaptive evolution in virulence effectors of the rice blast fungus Pyricularia oryzae

  Le Naour-Vernet M, Charriat F, Gracy J, Cros-Arteil S, Ravel S, Veillet F, Meusnier I, Padilla A, Kroj T, Cesari S, Gladieux P, PLoS Pathog, 2023

• SecretoMyc, a web-based database on mycobacteria secreted proteins and structure-based homology identification using bio-informatics tools

  Gracy J, Vallejos-Sanchez K, Cohen-Gonsaud M, Tuberculosis (Edinb), 2023

• A Mycobacterium tuberculosis Effector Targets Mitochondrion, Controls Energy Metabolism, and Limits Cytochrome cExit

  Martin M, deVisch A, Boudehen YM, Barthe P, Gutierrez C, Turapov O, Aydogan T, Heriaud L, Gracy J, Neyrolles O, Mukamolova GV, Letourneur F, Cohen-Gonsaud M, Microbiol Spectr, 2023

2022

• A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins

  Lazar N, Mesarich CH, Petit-Houdenot Y, Talbi N, Li de la Sierra-Gallay I, Zelie E, Blondeau K, Gracy J, Ollivier B, Blaise F, Rouxel T, Balesdent MH, Idnurm A, van Tilbeurgh H, Fudal I, PLoS Pathog, 2022

2021

• Programmable receptors enable bacterial biosensors to detect pathological biomarkers in clinical samples

  Chang HJ, Zuniga A, Conejero I, Voyvodic PL, Gracy J, Fajardo-Ruiz E, Cohen-Gonsaud M, Cambray G, Pageaux GP, Meszaros M, Meunier L, Bonnet J, Nat Commun, 2021

• Resolving the activation mechanism of the D99N antiterminator LicT protein

  Yang Y, Gracy J, Declerck N, Demene H, J Struct Biol, 2021

2020

• Structural Insights into of the Allosteric Activation of the LicT Antiterminator by PTS-Mediated Phosphorylation

  Yang Y, Padilla A, deGuillen K, Mammri L, Gracy J, Declerck N, Demene H, Structure, 2020

2019

• Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis

  Fleury C, Gracy J, Gautier MF, Pons JL, Dufayard JF, Labesse G, Ruiz M, de Lamotte F, PeerJ, 2019

2018

• KNOTTIN: the database of inhibitor cystine knot scaffold after 10 years, toward a systematic structure modeling

  Postic G, Gracy J, Perin C, Chiche L, Gelly JC, Nucleic Acids Res, 2018

2017

• Recognition of the Magnaporthe oryzae effector AVR-Pia by the decoy domain of the rice NLR immune receptor RGA5

  Ortiz D, deGuillen K, Cesari S, Chalvon V, Gracy J, Padilla A, Kroj T, Plant Cell, 2017

2015

• Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi

  deGuillen K, Ortiz-Vallejo D, Gracy J, Fournier E, Kroj T, Padilla A, PLoS Pathog, 2015

2011

• Structure and modeling of knottins, a promising molecular scaffold for drug discovery

  Gracy J, Chiche L, Curr Pharm Des, 2011

2010

• Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots

  Gracy J, Chiche L, BMC Bioinformatics, 2010

2008

• Knottin cyclization: impact on structure and dynamics

  Heitz A, Avrutina O, Le-Nguyen D, Diederichsen U, Hernandez JF, Gracy J, Kolmar H, Chiche L, BMC Struct Biol, 2008

• KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007

  Gracy J, Le-Nguyen D, Gelly JC, Kaas Q, Heitz A, Chiche L, Nucleic Acids Res, 2008

• Structure and folding of disulfide-rich miniproteins: insights from molecular dynamics simulations and MM-PBSA free energy calculations

  Combelles C, Gracy J, Heitz A, Craik DJ, Chiche L, Proteins, 2008

2005

• EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments

  Gelly JC, Chiche L, Gracy J, BMC Bioinformatics, 2005

• PAT: a protein analysis toolkit for integrated biocomputing on the web

  Gracy J, Chiche L, Nucleic Acids Res, 2005

2004

• Squash inhibitors: from structural motifs to macrocyclic knottins

  Chiche L, Heitz A, Gelly JC, Gracy J, Chau PT, Ha PT, Hernandez JF, Le-Nguyen D, Curr Protein Pept Sci, 2004

• The KNOTTIN website and database: a new information system dedicated to the knottin scaffold

  Gelly JC, Gracy J, Kaas Q, Le-Nguyen D, Heitz A, Chiche L, Nucleic Acids Res, 2004

2001

• Stepwise modelling optimization from sequence to quaternary structure

  Labesse G, Douguet D, Gracy J, Pons J, Chiche L, 4th European Symposium of The Protein Society, 2001

2000

• The Cystine-Stabilized Beta-sheet motif is a common and useful motif por protein engineering

  Heitz A, Le Nguyen D, Hernandez JF, Gracy J, Chiche L, Peptide 2000, 2000

1999

• Direct selection of EGF mutants displayed on filamentous phage using cells overexpressing EGF receptor

  Souriau C, Gracy J, Chiche L, Weill M, Biol Chem, 1999

1998

• DOMO: a new database of aligned protein domains

  Gracy J, Argos P, Trends Biochem Sci, 1998

• Automated protein sequence database classification. II. Delineation Of domain boundaries from sequence similarities

  Gracy J, Argos P, Bioinformatics, 1998

• Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment

  Gracy J, Argos P, Bioinformatics, 1998

1995

• Environnement d'apprentissage et modelisation structurale des proteines.

  Gracy J, Sallantin J, Technique et Science Informatiques, 1995

1993

• Improved alignment of weakly homologous protein sequences using structural information

  Gracy J, Chiche L, Sallantin J, Protein Eng, 1993

• Learning and alignment methods applied to protein structure prediction

  Gracy J, Chiche L, Sallantin J, Biochimie, 1993

• A modular learning environment for protein modeling

  Gracy J, Chiche L, Sallantin J, Proc Int Conf Intell Syst Mol Biol, 1993

• Statistical potentials and learning methods to evaluate protein models. Application to the coiled-coil tropomyosin

  Gracy J, Cregut D, Chiche L, THEOCHEM, 1993