Professeur
Mail : fyd@u-picardie.fr
Tel : 03 22 82 74 98
Fax : 03 22 82 74 69
C.V.

 

Site Web : http://q4md-forcefieldtools.org/FyD/ (q4md-forcefieldtools, a web site designed for empirical force field development: Application to the structural studies of biomolecules.)

Membre de l'équipe THERA

Description des travaux de recherche

• Bioinformatique :  Développement de programmes, de base de données et de tutoriels utiles pour le calcul de charges atomiques et de paramètres de champs de forces, outils disponibles à partir du site Internet http://q4md-forcefieldtools.org.
• Champ de forces :  Développement de champs de forces pour biomolécules (oligonucléotides, oligosaccharides et oligopeptides inhabituels, structures organiques et complexants de métaux).
• Etude structurale de biomolécules :  Etudes réalisées par dynamique moléculaire en présence de solvant implicite ou explicite impliquant diverses biomolécules modèles (acides nucléiques artificiels, oligosaccharides multivalents et cyclodextrines modifiées, hétérocycles et calixarènes complexant potentiels du Fer).

Publications

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  [1] E. Vanquelef, S. Simon, G. Marquant, E. Garcia, G. Klimerak, J.C. Delepine, P. Cieplak, F.-Y. Dupradeau, R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments, Nucleic Acids Res., 39 (2011) W511-W517.

• 
  [2] C. Cezard, X. Trivelli, F. Aubry, F. Djedaini-Pilard, F.-Y. Dupradeau, Molecular dynamics studies of native and substituted cyclodextrins in different media: 1. Charge derivation and force field performances, Phys. Chem. Chem. Phys., 13 (2011) 15103-15121.

• 
  [3] S. Abel, F.-Y. Dupradeau, E.P. Raman, A.D. MacKerell, M. Marchi, Molecular Simulations of Dodecyl-β-maltoside Micelles in Water: Influence of the Headgroup Conformation and Force Field Parameters, J. Phys. Chem. B, 115 (2011) 487-499.

• 
  [4] S.G. Gouin, F.J.M. Garcia, E. Vanquelef, F.-Y. Dupradeau, E. Salomonsson, H. Leffler, M. Ortega-Munoz, U.J. Nilsson, J. Kovensky, Multimeric Lactoside "Click Clusters" as Tools to Investigate the Effect of Linker Length in Specific Interactions with Peanut Lectin, Galectin-1, and -3, ChemBioChem, 11 (2010) 1430-1442.

• 
  [5] F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski, P. Cieplak, The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building, Phys. Chem. Chem. Phys., 12 (2010) 7821-7839.

• 
  [6] P. Cieplak, F.-Y. Dupradeau, Y. Duan, J. Wang, Polarization effects in molecular mechanical force fields, J. Phys.: Condens. Matter, 21 (2009) 333102/333101-333102/333121.

• 
  [7] F.-Y. Dupradeau, S. Pissard, M.-P. Coulhon, E. Cadet, K. Foulon, C. Fourcade, M. Goossens, D.A. Case, J. Rochette, An unusual case of hemochromatosis due to a new compound heterozygosity in HFE (p.
  [Gly43Asp;His63Asp]+
  [Cys282Tyr]): structural implications with respect to binding with transferrin receptor 1, Hum Mutat, 29 (2008) 206.

• 
  [8] F.-Y. Dupradeau, C. Cezard, R. Lelong, E. Stanislawiak, J. Pecher, J.C. Delepine, P. Cieplak, R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries, Nucleic Acids Res., 36 (2008) D360-D367.

• 
  [9] P. Cieplak, F.-Y. Dupradeau, Including polarization effects in the RESP charge derivation method, in, American Chemical Society, 2008, pp. COMP-369.

• 
  [10] J. Chen, F.-Y. Dupradeau, D.A. Case, C.J. Turner, J. Stubbe, DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics, Nucleic Acids Res., 36 (2008) 253-262.

• 
  [11] C. Cezard, E. Vanquelef, J. Pecher, P. Sonnet, P. Cieplak, E. Derat, F.-Y. Dupradeau, RESP charge derivation and force field topology database generation for complex bio-molecular systems and analogs, in, American Chemical Society, 2008, pp. COMP-267.

• 
  [12] S.G. Gouin, E. Vanquelef, F.J.M. Garcia, M.C. Ortiz, F.-Y. Dupradeau, J. Kovensky, Multi-Mannosides Based on a Carbohydrate Scaffold: Synthesis, Force Field Development, Molecular Dynamics Studies, and Binding Affinities for Lectin Con A, J. Org. Chem., 72 (2007) 9032-9045.

• 
  [13] J. Chen, F.-Y. Dupradeau, D.A. Case, C.J. Turner, J. Stubbe, Nuclear Magnetic Resonance Structural Studies and Molecular Modeling of Duplex DNA Containing Normal and 4'-Oxidized Abasic Sites, Biochemistry, 46 (2007) 3096-3107.

• 
  [14] J. Pecher, F.G. Le, P. Bogdanowicz, J.-P. Pujol, D.A. Case, J. Rochette, F.-Y. Dupradeau, Towards the solution structure of a "mini-insulin", in, American Chemical Society, 2005, pp. COMP-149.

• 
  [15] C. Ka, G.G. Le, F.-Y. Dupradeau, J. Rochette, C. Ferec, The Q283P amino-acid change in HFE leads to structural and functional consequences similar to those described for the mutated 282Y HFE protein, Hum. Genet., 117 (2005) 467-475.

• 
  [16] F.-Y. Dupradeau, C. Yu, R. Jimenez, F.E. Romesberg, D.A. Case, Tautomerization of the HBO base pair model in the DNA major and minor grooves, in, American Chemical Society, 2005, pp. COMP-223.

• 
  [17] F.-Y. Dupradeau, D.A. Case, C. Yu, R. Jimenez, F.E. Romesberg, Differential Solvation and Tautomer Stability of a Model Base Pair within the Minor and Major Grooves of DNA, J. Am. Chem. Soc., 127 (2005) 15612-15617.

• 
  [18] A. Pigache, P. Cieplak, F.-Y. Dupradeau, Automatic and highly reproducible RESP and ESP charge derivation: Application to the development of programs RED and X RED, in, American Chemical Society, 2004, pp. COMP-181.

• 
  [19] J.U.O. Mayo, F.-Y. Dupradeau, D. Guillaume, J.-L. Fourrey, P. Clivio, γ-Radiolysis DNA Products: Synthesis of 6-(α-Thyminyl)-5,6-dihydro-4-thiothymine Derivatives, J. Org. Chem., 69 (2004) 4797-4801.

• 
  [20] G.G. Le, F.-Y. Dupradeau, C. Mura, S. Jacolot, V. Scotet, G. Esnault, A.-Y. Mercier, J. Rochette, C. Ferec, Phenotypic expression of the C282Y/Q283P compound heterozygosity in HFE and molecular modeling of the Q283P mutation effect, Blood Cells, Mol., Dis., 30 (2003) 231-237.

• 
  [21] F.-Y. Dupradeau, J. Rochette, Bugs in computational chemistry software and their consequences: the importance of the source code, J. Mol. Model., 9 (2003) 271-272.

• 
  [22] F.G. Le, F.-Y. Dupradeau, J.-P. Pujol, J.-P. Monti, P. Bogdanowicz, Synthesis, and functional properties of a modified human insulin A-Chain: implication in a 'Mini-Insulin' structure determination, Bioorg. Med. Chem., 10 (2002) 2111-2117.

• 
  [23] F.-Y. Dupradeau, P. Sonnet, D. Guillaume, H.M. Senn, P. Clivio, Ab Initio Study of the (5R)- and (5S)-TT Pyrimidine h5(6-4) Pyrimidone Photoproducts. Implications on the Design of New Biologically Relevant Analogues, J. Org. Chem., 67 (2002) 9140-9145.

• 
  [24] F.Y. Dupradeau, T. Richard, F.G. Le, H. Oulyadi, Y. Prigent, J.P. Monti, A new B-chain mutant of insulin: comparison with the insulin crystal structure and role of sulfonate groups in the B-chain structure, J. Pept. Res., 60 (2002) 56-64.

• 
  [25] J.S.D. Kumar, F.-Y. Dupradeau, M.J. Strouse, M.E. Phelps, T. Toyokuni, Electrophilic Azidation for Stereoselective Synthesis of 2-Azido-2-deoxyaldono-1,5-lactones, J. Org. Chem., 66 (2001) 3220-3223.

• 
  [26] A. Dejoux, P. Cieplak, N. Hannick, G. Moyna, F.-Y. Dupradeau, AmberFFC, a flexible program to convert AMBER and GLYCAM force fields for use with commercial molecular modeling packages, J. Mol. Model., 7 (2001) 422-432.

• 
  [27] F.Y. Dupradeau, B. Altenberg-Greulich, R. Warin, V. Fuentes, J.P. Monti, J. Rochette, A 3-dimensional model building by homology of the HFE protein: molecular consequences and application to antibody development, Biochim. Biophys. Acta, Protein Struct. Mol. Enzymol., 1481 (2000) 213-221.