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Accueil du site > Équipes > Arômes Parfums Synthèse Modélisation > Thème Modélisation Moléculaire

Thème Modélisation Moléculaire

Publications/brevets


2016



2015


 

2014


  • C.A. de March and J. Golebiowski. A computational microscope focused on the sense of smell. Biochimie, 2014, 107A, 3-10
  • J. Topin, C.A. de March, L. Charlier, C. Ronin, S. Antonczak, J. Golebiowski. Discrimination between Olfactory Receptors agonists and non-agonists. Chemistry, a European Journal, 2014 ,20, 10227-10230
  • C. Delasalle, C.A.de March, U. Meierhenrich, H. Brevard, J. Golebiowski, N. Baldovini. Structure-odor Relationships of β-Santalol analogues Chem. Biodiv, 2014, 11, 1843-1860
  • Topin, J., Diharce, J. Fiorucci, S., Antonczak, S. Golebiowski, J. O2 migration rates in [NiFe] hydrogenases. A joint approach combining free-energy calculations and kinetic modeling. J. Phys Chem. B., 2014, 118 (3), 676–681
  • Le Breton, N., Martinho M., Kuanysh K., Topin, J., Mileo, E., Blocquel, D., Habchi, J., Longhi, S., Rockenbauer, A., Golebiowski, J., Guigfliarelli, B., Marque, S., Belle, V. Diversification of EPR signatures in site directed spin labeling using a beta-phosphorylated nitroxide. PhysChemChemPhys, 2014, 16, 4202-4209
  • I. Kufareva, V. Katritch, Participants of GPCR Dock 2013#,R.C. Stevens, R. Abagyan Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment : Meeting New Challenges. Structure. 2014, 22, 1120-1139
  • S. Fiorucci*, M. Zacharias. Chap. 20 : Computational antigenic epitope prediction by calculating electrostatic desolvation penalties of protein surface. in Immunoinformatics, R.K. De, N. Tomar, Springer (2014) p.365-374
  • F. Julien, S. Moja, A. Bony, S. Legrand, C. Petit, T. Benabdelkader, K. Poirot, S. Fiorucci, Y. Guitton, F. Nicole, S. Baudino, J.L.Magnard. Isolation and functional characterization of a t-cadinol synthase, a new sesquiterpene synthase from Lavandula angustifolia. Plant Mol. Biol., 2014, 84, 227-241.
 

2013


  • JM. Heydel, AM. Le Bon, P. Faure, F. Neiers, Y. Artur, J. Golebiowski, L. Briand Odorant-binding proteins and xenobiotic metabolizing enzymes : implications in olfactory peri-receptor events. Anatomical Record, 2013
  • J. Golebiowski, L. Charlier, J. Topin, S. Fiorucci, S. Antonczak Molecular features underlying the chemoreception of Odorant binding Proteins and Olfactory Receptors. Insights from molecular modeling and biophysical data. Chapter 96, in Flavour Sciences, 2013, 519-524
  • Charlier L, Topin J, de March CA, Lai PC, Crasto CJ, Golebiowski J. Molecular modelling of odorant/olfactory receptor complexes Methods Mol Biol. 2013 ;1003:53-65
  • N. Parassol, C. Bienvenu, C. Boglio, S. Fiorucci, D. Cerezo, X.M. Yu, G. Godeau, J. Greiner, P. Vierling, S. Noselli, C. Di Giorgio, V. Van de Bor. In vivo characterization of dynein-driven nanovectors using Drosophila oocytes. PlosOne, 2013, 8, e82908
 

2012


  • L. Charlier, J. Topin, C. Ronin, SK. Kim, WA. Goddard III, R. Efremov, J. Golebiowski How broadly tuned olfactory receptors equally recognize their agonists. Human OR1G1 as a test case. Cellular and Molecular Life Sciences, 2012, 69, 4205-4213
  • J. Golebiowski,* J. Topin, L. Charlier, L. Briand Interaction between odorants and proteins involved in the perception of smell. The case of Odorant-Binding Proteins probed by molecular modeling and biophysical data. Flavour and Fragrance Journal, 2012, 27, 445-453
  • J. Golebiowski, X. Fernandez Chimie des substances odorantes et physiologie de l’olfaction. 15 pages in « Les Huiles Essentielles. Tradition et Innovation ». 2012
  • J. Topin, M. Rousset, S. Antonczak, J. Golebiowski* Kinetics and thermodynamics of gas diffusion in a NiFe hydrogenase. Proteins Structure Function and Bioinformatics, 2012, 80, 677–682
  • M.Maïbèche, JM. Heydel, AM. Le Bon, J. Golebiowski, L. Briand Chap. 3.2. Périrécéption et protéines porteuses (Perireception and Odorant Binding Proteins) 9 pages in “ODORAT et GOUT : de la neurobiologie des sens chimiques aux applications agronomiques, industrielles et médicales” (380 pages), QUAE Ed. 2012
  • S. Schneider, A. Saladin, S. Fiorucci, C. Préviost, M. Zacharias, ATTRACT and PTools : Open sources programs for protein-protein docking. Chapter 15 in Computational Drug Discovery and Design, R. Baron, Springer (2012) p.221-232
 

2011


  • J. Golebiowski, S. Fiorucci, M. Adrian-Scotto, J. Fernandez-Carmona, S. Antonczak Molecular features underlying the perception of astringency as probed by molecular modeling. Molecular informatics, 2011, 30, 410-414
 

2010


  • S. Fiorucci, S. Antonczak, J. Golebiowski. Prediction/calculation of protein-protein binding affinities and mutation effects, Chapter 11, in Protein-protein complexes:Analysis, modelling and drug design. M. Zacharias Ed. imperial Press 2010
  • C. Roucairol, S. Azoulay, M.C. Nevers, J. Golebiowski, C. Créminon, J. Grassi, A. Burger, D. Duval. Design, synthesis and studies of triphosphate analogues for the production of anti AZT-TP antibodies. Bioorganic & Medicinal Chemistry Letters, 2010, 20,987-990
  • M. Soriani, P. Petit, R. Grifantini, R. Petracca, G. Gancitano, E. Frigimelica, F. Nardelli, C. Garcia, S. Spinelli, G. Scarabelli, S. Fiorucci, R. Affentranger, M. Ferrer-Navarro, M. Zacharias, G. Colombo, L. Vuillard, X. Daura and G. Grandi. Exploiting antigenic diversity for vaccines design : the Chlamydia ArtJ paradigm. J. Biol. Chem, 2010, 285, 30126-30138.
  • S. Fiorucci, M. Zacharias. Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT. Proteins, 2010, 78(15), 3131-3139
  • S. Fiorucci, M. Zacharias. Prediction of protein-protein interaction sites using electrostatic desolvation profile. Biophys J. 2010, 98(9), 1921-1930.
 

2009


  • L. Charlier, D. Cabrol-Bass, J. Golebiowski . How does human odorant binding protein bind odorants ? The case of aldehydes studied by molecular dynamics. C.R Chimie, 2009, 12, 905-910
  • S. Antonczak, S. Fiorucci, J. Golebiowski, D. Cabrol-Bass. Theoretical investigations of the role played by Quercetinase Enzymes upon flavonoids oxygenolsysis mechanism. PhysChemChemPhys,2009, 11, 1491-1501
  • A. Saladin, S. Fiorucci, P. Poulain, C. Prevost, M. Zacharias. PTools : an opensource molecular docking library. BMC Struct. Biol, 2009, 9, 27.
 

2008


  • L. Charlier, S. Antonczak, E. Jacquin-joly, D. Cabrol-Bass, J. Golebiowski. Deciphering the selectivity of Bombyx mori pheromone binding protein for bombykol over bombykal. A theoretical approach. ChemPhysChem 2008,9, 2785-2793
  • S. Fiorucci ; J. Golebiowski ; D. Cabrol-Bass ; S. Antonczak . Molecular Simulations enlighten the binding mode between quercetine and lipoxygenase-3. PROTEINS : Structure, Function, and Bioinformatics, 2008,73, 290-298
 

2007


  • L. Charlier ; C. Nespoulous, S. Fiorucci, S. Antonczak ; J. Golebiowski Binding free energy prediction in strongly hydrophobic systems. Physical Chemistry Chemical Physics, 2007,9,5761-5771 .
  • S. Fiorucci ; J. Golebiowski ; D. Cabrol-Bass ; S. Antonczak . Molecular Simulations bring new insights into Flavonoid/Quercetinase Interaction Modes. PROTEINS : Structure, Function, and Bioinformatics, 2007, 67, 961-970
  • J. Golebiowski, S. Antonczak, S. Fiorucci, D. Cabrol-Bass Molecular mechanism underlying Odorant Binding Protein chemoreception. PROTEINS : Structure, Function, and Bioinformatics, 2007, 67, 448-458
  • S. Fiorucci ; J. Golebiowski ; D. Cabrol-Bass ; S. Antonczak. DFT Study of Quercetin Activated Forms Involved in Antiradical, Antioxidant, and Prooxidant Biological Processes. Journal of Agricultural Food and Chemistry, 2007, 55, 903-911
  • F. Berrue, O. P. Thomas, R. Laville, S. Prado, J. Golebiowski, R. Fernandez and P. Amade The marine sponge Plakortis zyggompha : a source of original bioactive polyketides. Tetrahedron, 2007, 63, 2328-2334
 

2006


  • S. Antoniotti, J. Golebiowski, D. Cabrol-Bass, E. Dunach Density functional theory investigations on acid-catalysed epoxide oxidative ring-opening by DMSO. Competition between oxidation processes. Journal of Molecular Structure THEOCHEM, 763, 2006 155-159
  • S. Fiorucci, J. Golebiowski, D. Cabrol-Bass, S. Antonczak Molecular Simulations reveal a new entry site in Quercetin 2,3-Dioxygenase. A pathway for dioxygen ?PROTEINS : Structure, Function, and Bioinformatics, 64, 2006, 845-850
  • J. Golebiowski, S. Antonczak, D. Cabrol-Bass Molecular dynamics studies of odorant binding protein free of ligand and complexed to pyrazine and octenol. Journal of Molecular Structure THEOCHEM, 763, 2006, 165-174
 

2005


  • U.J. Meierhenrich, J. Golebiowski, X. Fernandez, D. Cabrol-Bass De la molécule à l’odeur. (From a molecule to an odour) L’Actualité Chimique, septembre 2005, 29-40
 

2004


  • U.J. Meierhenrich, J. Golebiowski, X. Fernandez, D. Cabrol-Bass The molecular basis of olfactory chemoreception. Angew. Chem. Int. Ed. Engl. 43, 2004, 6410-6412 ; Angew. Chem. 116, 2004, 6570-6573
  • J. Golebiowski, S. Antonczak, J. Fernandez-Carmona, R. Condom, D. Cabrol-Bass Closing loop base pairs in RNA loop-loop complexes. Structural behaviour, interaction energy and solvation analysis through molecular dynamics simulations. Journal of Molecular Modeling , 10, 2004, 408-417
  • S. Antoniotti, S. Antonczak, J. Golebiowski Acid-Catalysed Oxidative Ring-Opening of Epoxide by DMSO. Theoretical Investigations on the Effect of Acid Catalysts and Substituents.Theoretical Chemistry Account, 112, 2004, 290 - 297
  • S. Fiorucci, J. Golebiowski, D. Cabrol-Bass, S. Antonczak Oxygenolysis of Flavonoid compounds. DFT Description of the Mechanism for Quercetin ChemPhysChem 2004, 5,1726-1733
  • J. Golebiowski, S. Antonczak, A. di-Giorgio, R. Condom, D. Cabrol-Bass Molecular Dynamics Simulation of Hepatis C Virus IRES IIId Domain : Structural Behaviour, Electrostatic and energetic Analysis. Journal of Molecular Modeling, 10, 2004, 60-68
 

2002


  • Golebiowski, J. ; Lamare, V., Ruiz-Lopez, M. F. Rb/Cs selectivity between Benzo21crown7 and riBenzo21Crown7. An ab initio study. Journal of Computational Chemistry 2002, 23(7), 724-731
  • Golebiowski, J. ; Lamare, V., Ruiz-Lopez, M. F. Quantum mechanical calculations on alkali complexes, in Calix2001. Chap. 18. Z. Asfari ; V. Böhmer ; J.M. Harrowfield ; J. Vicens eds. Kluwer Academic, Dordrecht. 2002