Publications

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D
Delalande O., Férey N, Laurent B., Gueroult M., Hartmann B., Baaden M.  2010.  Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device. Pac. Symp. Biocomput.. :205–215.
Decker H., Robert C.H, Gill S.J.  1987.  Nesting- An extension of the MWC model and its application to tarantula hemocyanin. Invertebrate Oxygen Carriers.
Decker H, Connelly PR, Robert CH, Gill SJ.  1988.  Nested allosteric interaction in tarantula hemocyanin revealed through the binding of oxygen and carbon monoxide. Biochemistry. 27:6901–6908.
De Vecchis D, Cavellini L, Baaden M, Hénin J, Cohen MM, Taly A.  2017.  A membrane-inserted structural model of the yeast mitofusin Fzo1. Sci Rep. 7(1):10217.
De Vecchis D, Brandner A, Baaden M, Cohen MM, Taly A.  2019.  A molecular perspective on mitochondrial membrane fusion: from the key players to oligomerization and tethering of mitofusin. The Journal of membrane biology. 252:293–306.
De Simone A, Zagari A, Derreumaux P.  2007.  Structural and hydration properties of the partially unfolded states of the prion protein. Biophys. J.. 93:1284–1292.
De Simone A, Derreumaux P.  2010.  Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: A replica exchange molecular dynamics study in explicit solvent. J. Chem. Phys.. 132:165103.
de Oliveira DMendes, Zukowski SR, Palivec V, Hénin J, Martinez-Seara H, Ben-Amotz D, Jungwirth P, Duboué-Dijon E.  2020.  Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy. Phys. Chem. Chem. Phys.. 22:24014-24027.
Dauchez M, LAGANT P, Derreumaux P, VERGOTEN G, SEKKAL M, SOMBRET B.  1994.  FORCE-FIELD AND VIBRATIONAL-SPECTRA OF OLIGOSACCHARIDES WITH DIFFERENT GLYCOSIDIC LINKAGES .2. MALTOSE MONOHYDRATE, CELLOBIOSE AND GENTIOBIOSE. Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy. 50:105–118.
Dauchez M, Derreumaux P, VERGOTEN G.  1993.  VIBRATIONAL MOLECULAR-FORCE FIELD OF MODEL COMPOUNDS WITH BIOLOGIC INTEREST .2. HARMONIC DYNAMICS OF BOTH ANOMERS OF GLUCOSE IN THE CRYSTALLINE STATE. J. Comput. Chem.. 14:263–277.
Dauchez M, Derreumaux P, LAGANT P, VERGOTEN G, SEKKAL M, LEGRAND P.  1994.  FORCE-FIELD AND VIBRATIONAL-SPECTRA OF OLIGOSACCHARIDES WITH DIFFERENT GLYCOSIDIC LINKAGES .1. TREHALOSE DIHYDRATE, SOPHOROSE MONOHYDRATE AND LAMINARIBIOSE. Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy. 50:87–104.
Dauchez M, Derreumaux P, LAGANT P, VERGOTEN G.  1995.  A VIBRATIONAL MOLECULAR-FORCE FIELD OF MODEL COMPOUNDS WITH BIOLOGICAL INTEREST .4. PARAMETERS FOR THE DIFFERENT GLYCOSIDIC LINKAGES OF OLIGOSACCHARIDES. J. Comput. Chem.. 16:188–199.
Darre L., Tek A., Baaden M, Pantano S..  2012.  Mixing atomistic and coarse grain solvation models for MD simulations: let WT4 handle the bulk. Jctc.
Danilowicz C, Hermans L, Coljee V, Prévost C, Prentiss M.  2017.  ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences. Nucleic Acids Res. 45:8448-8462.
Danilowicz C, Yang D, Kelley C, Prévost C, Prentiss M.  2015.  The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing recognition in vivo. Nucleic Acids Res.. 43:6473–85.
Danilowicz C, Vietorisz E, Godoy-Carter V, Prévost C, Prentiss M.  2021.  Influences of ssDNA-RecA Filament Length on the Fidelity of Homologous Recombination. Journal of Molecular Biology. 433:167143.
da Silva FLuis Barro, Derreumaux P, Pasquali S.  2017.  Protein-RNA complexation driven by the charge regulation mechanism.. Biochem Biophys Res Commun.
da Silva FLuis Barro, Derreumaux P, Pasquali S.  2017.  Fast coarse-grained model for RNA titration.. J Chem Phys. 146(3):035101.
da Silva FLuis Barro, Pasquali S, Derreumaux P, Dias LGustavo.  2016.  Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin. Soft Matter. 12:5600–5612.
da Silva FLuis Barro, Sterpone F, Derreumaux P.  2019.  OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field. Journal of Chemical Theory and Computation. 15:3875-3888.
C
Cubellis M.V, Baaden M, Andreotti G..  2015.  Taming molecular flexibility to tackle rare diseases. Biochimie. 113:54–58.
Cragnolini T, Laurin Y, Derreumaux P, Pasquali S.  2015.  Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings. J. Chem. Theory Comput.. 11:3510–3522.
Cragnolini T, Derreumaux P, Pasquali S.  2013.  Coarse-Grained Simulations of RNA and DNA Duplexes. J. Phys. Chem. B. 117:8047–8060.
Cragnolini T, Chakraborty D, Sponer J, Derreumaux P, Pasquali S, Wales DJ.  2017.  Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch.. J Chem Phys. 147(15):152715.
Cragnolini T, Laurin Y, Derreumaux P, Pasquali S.  2014.  Coarse-Grain RNA Folding: Towards More Complex Structures. Biophys. J.. 106:283A.

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