FyD Home Page



Force Field Parameter Development

RESP ESP charge Derive

RESP ESP charge DDataBase

RESP ESP charge Derive Server Development


Full list of publications

2016   2014   2013   2012   2011   2010   2009   2008   2007   2005   2004-2001   2000-1997   1996-1993


J.-P. Becker, F. Wang, P. Sonnet and F.-Y. Dupradeau, β-Hematin Crystal Formation: New Insights from Molecular Dynamics Simulations of Small Clusters in Condensed Phase, Cryst. Growth Des. 2016, 16, 2249-2259, [PMID], [Local PDF file].


S. Abel, A. Lorieau, B. de Foresta, F.-Y. Dupradeau and M. Marchi, Bindings of hMRP1 Transmembrane Peptides with Dodecylphosphocholine and Dodecyl-β-maltoside Micelles: A Molecular Dynamics Simulation Study, BBA-Biomembranes 2014, 1838, 493-509, [PMID], [Local PDF file].


J.M. Sanders, M.E. Wampole, C.-P. Chen, D. Sethi, A. Singh, F.-Y. Dupradeau, F. Wang, B.D. Gray, M.L. Thakur and E. Wickstrom, Effects of Hypoxanthine Substitution in Peptide Nucleic Acids Targeting KRAS2 Oncogenic mRNA Molecules: Theory and Experiment, J. Phys. Chem. B. 2013, 117, 11584-11595, [PMID], [Local PDF file].


P. Rouge, A. Dassonville-Klimpt, C. Cezard, S. Boudesocque, R. Ourouda, C. Amant, F. Gaboriau, I. Forfar, J. Guillon, E. Guillon, E. Vanquelef, P. Cieplak, F.-Y. Dupradeau, L. Dupont and P. Sonnet, Synthesis, Physicochemical Studies, Molecular Dynamics Simulations and Metal-Ion-Dependent Antiproliferative and Antiangiogenic Properties of Cone ICL670-Substituted Calix[4]arenes, ChemPlusChem 2012, 77, 1001-1016, [PMID], [Local PDF file].

S. Abel, F.-Y. Dupradeau, and M. Massimo, Molecular dynamics simulations of a characteristic DPC micelle in water, J. Chem. Theory Comput. 2012, 8, 4610-4623, [PMID], [Local PDF file].


C. Cézard, X. Trivelli, F. Aubry, F. Djedaini-Pilard and 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. 2011, 13, 15103-15121, [PMID], [Local PDF file].

E. Vanquelef, S. Simon, G. Marquant, E. Garcia, G. Klimerak, J. C. Delepine, P. Cieplak and 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, Nucl. Acids Res. (Web server issue) 2011, 39, W511-W517, [PMID], [PMCID], [Local PDF file].

S. Abel, F.-Y. Dupradeau, R. E. Prabu, A. D. MacKerell and M. Massimo, Molecular simulations of Dodecyl-β-maltosidemicelles in water: Influence of the headgroup conformation and force field parameters, J. Phys. Chem. B. 2011, 115, 487-499, [PMID], [PMCID], [Local PDF file].


F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski and P. Cieplak, The R.E.D. tools: Advances in RESP and ESP charge derivation and force field library building, Phys. Chem. Chem. Phys. 2010, 12, 7821-7839, [PMID], [PMCID], [Local PDF file], One of the top ten most-read articles from the online version of PCCP for July 2010.

S. G. Gouin, J. M. Garcia Fernandez, E. Vanquelef, F.-Y. Dupradeau, E. Salomonsson, H. Leffler, F. Santoyo-Gonzalez, U. J. Nilsson and 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, 2010, 11, 1430-1442, [PMID], [Local PDF file].


P. Cieplak, F.-Y. Dupradeau, Y. Duan and J. Wang, Polarization effects in molecular mechanical force fields, J. Phys.: Condens. Matter, 2009, 21, 333102, [Abstract], [Local PDF file].


F.-Y. Dupradeau, S. Pissard, M. P. Coulhon, E. Cadet, K. Foulon, C. Fourcade, M. Goossens, D. A. Case and J. Rochette, An unusual compound heterozygosity in HFE Hemochromatosis (p.G43D-H63D/p.C282Y): Structural implications with respect to binding with transferrin receptor 1, Hum. Mutat., 2008, 29, 206, [PMID], [Local PDF file].

F.-Y. Dupradeau, C. Cézard, R. Lelong, E. Stanislawiak, J. Pecher, J. C. Delepine and P. Cieplak, R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries, Nucl. Acids Res. (Database issue), 2008, 36, D360-D367, [PMID], [PMCID], [Local PDF file].

J. Chen, F.-Y. Dupradeau, D. A. Case, C. J. Turner and J. Stubbe, DNA oligonucleotides with A, T, G, or C opposite an abasic site: Structure and dynamics, Nucl. Acids Res., 2008, 36, 253-262, [PMID], [PMCID], [Local PDF file].


S. G. Gouin, E. Vanquelef, J. M. Garcia Fernandez, C. Ortiz Mellet, F.-Y. Dupradeau and J. Kovensky, Multi-mannosides based on carbohydrate scaffold: synthesis, force field development, molecular dynamics studies and binding affinities for the lectin ConA, J. Org. Chem., 2007, 72, 9032-9045, [PMID], [Local PDF file].

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


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

C. Ka, G. Le Gac, F.-Y. Dupradeau, J. Rochette and 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., 2005, 117, 467-475, [PMID], [Local PDF file].


J.U. Ortiz Mayo, F.-Y. Dupradeau, D. Guillaume, J.-L. Fourrey and P. Clivio, G-Radiation induced DNA-damaged products: Synthesis of 6-(a-thyminyl)-5,6-dihydro-4-thiothymine derivatives, J. Org. Chem., 2004, 69, 4797-4801, [PMID], [Local PDF file].

F.-Y. Dupradeau and J. Rochette, Bugs in Computational Chemistry Software and their Consequences: The Importance of the Source Code, J. Mol. Model., 2003, 9, 271-272, [PMID], [Local PDF file].

G. Le Gac, F.-Y. Dupradeau, C. Mura, S. Jacolot, V. Scotet, G. Esnault, A. Y. Mercier, J. Rochette and C. Ferec, Phenotypic Expression of the C282Y/Q283P Compound Heterozygosity in HFE and Molecular Modeling of the effect of the Q283P mutation, Blood Cell. Mol. Dis., 2003, 30, 231-237, [PMID], [Local PDF file].

F.-Y. Dupradeau, P. Sonnet, D. Guillaume, H. M. Senn and 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., 2002, 67, 9140-9145, [PMID], [Local PDF file].

F.-Y. Dupradeau, T. Richard, G. Le Flem, H. Oulyadi, Y. Prigent and 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., 2002, 60, 56-64, [PMID], [Local PDF file].

G. Le Flem, F.-Y. Dupradeau, J.-P. Pujol, J.-P. Monti, and P. Bogdanowicz, Synthesis, and Functional Properties of a Modified Human Insulin A-Chain: Implication in a "Mini-insulin" Structure Determination, Bioorg. Med. Chem., 2002, 10, 2111-2117, [PMID], [Local PDF file].

A. Dejoux, P. Cieplak, N. Hannick, G. Moyna, and F.-Y. Dupradeau, AmberFFC, A Flexible Program to Convert AMBER and GLYCAM Force Fields for use with Commercial Molecular Modeling Packages, J. Mol. Model., 2001, 7, 422-432, [Abstract], [Local PDF file].

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


F.-Y. Dupradeau, B. Altenberg-Greulich, R. Warin, V. Fuentes, J.-P. Monti and J. Rochette, A 3-Dimensional Model Building by Homology of the HFE Protein : Molecular Consequences and Application to Antibody Development, Biochim. Biophys. Acta, 2000, 1481, 213-221, [PMID], [Local PDF file].

F.-Y. Dupradeau, F. Gaillard, and J.-M. Beau, Reduction of Azido-oligosaccharides to Amino(acetamino)sugars: A Samarium Diiodide-Water System, Carbohydrate Lett., 1999, 3, 317-322, [Local PDF file].

F.-Y. Dupradeau, G. Le Flem, J.-M. Wieruszeski, M. Calin, V. Larreta-Garde, and J.-P. Monti, Glycerol's influence on the oxidized insulin B-chain conformation in relation to the selectivity variation of subtilisin: an nuclear magnetic resonance and simulated annealing study, Biochim. Biophys. Acta, 1999, 1429, 446-458, [PMID], [Local PDF file].

S. Baltora-Rosset, A. Aboubecker, F.-Y. Dupradeau, E. Pauthe, V. Larreta-Garde, G.-A. Gacel and J.-P. Monti, Structural Studies by 1H NMR and Molecular Modeling of Peptide Substrates of Thermolysin in Relation with its Proteasic Activity in Water and Glycerol, J. Biomol. Struct. Dyn., 1999, 16, 1061-1074, [PMID], [Local PDF file].

F.-Y. Dupradeau, G. Le Flem, J.-M. Wieruszeski, M. Dauchez, A. Alix, V. Larreta-Garde, and J.-P. Monti, Structural modifications of the oxidized insulin B-chain induced by glycerol addition, Lett. Pept. Sci., 1997, 4, 489-495, [Abstract], [Local PDF file].

S. Baltora-Rosset, D. Marty, F.-Y. Dupradeau, E. Pauthe, V. Larreta-Garde, G. A. Gacel and J.-P. Monti, Micro-environment effect on the structure of synthetic substrates of Thermolysin, Lett. Pept. Sci., 1997, 4, 391-395, [Abstract], [Local PDF file].


F.-Y. Dupradeau, J. Prandi, and J.-M. Beau, Synthesis of the 2,6-Dideoxy-4-S-Methyl-4-thio-D-ribo-Hexopyranose, A component of the Esperamicin oligosaccharide, Tetrahedron, 1995, 51, 3205-322, [Abstract], [Local PDF file].

F.-Y. Dupradeau, S.-i. Hakamori and T. Toyokuni, Electrophilic azidation of 2-Deoxy-aldono-1,5-lactones : an Alternative Route to 2-Azido-2-deoxy-aldopyranoses, J. Chem. Soc. Chem. Commun., 1995, 2, 221-222, [Abstract], [Local PDF file].

F.-Y. Dupradeau, M. R. Stroud, D. Boivin, L. Li, S.-i. Hakamori, A. K. Singhal and T. Toyokuni, Solid-Phase Synthesis and Immunoreactivity of Penta-O-(N-Acetyl-α-D-Galactosaminyl)-MUC1 Eicosapeptide, A Glycosylated Counter Part of The Highly Immunogenic Tandem Repeat Sequence of Carcinoma-Associated Mucin, Bioorg. Med. Chem. Lett., 1994, 4, 1813-1818, [Abstract], [Local PDF file].

F.-Y. Dupradeau, J. Prandi, S. Allaire and J.-M. Beau, Two Synthesis of the 2,4,6-Trideoxy-4-methylthio-D-ribo-pyranose, Tetrahedron Lett., 1993, 34, 4513-4516, [Abstract], [Local PDF file].

Valid XHTML 1.0 Strict CSS Valide !

Last update of this page: April 15th, 2016.