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Force Field Parameter Development

RESP ESP charge Derive

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Full list of publications

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


2016

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].

2014

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].

2013

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].

2012

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].

2011

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].

2010

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].

2009

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].

2008

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].

2007

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].

2005

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].

2004-2001

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].

2000-1997

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].

1996-1993

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].


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