Publications

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Graf J, Nguyen PH, Stock G, Schwalbe H.  2007.  Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study. J. Am. Chem. Soc.. 129:1179–1189.
Nguyen PH, Mu YG, Stock G.  2005.  Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study. Proteins: Struct., Funct., Bioinf.. 60:485–494.
Baaden M, Barboiu M, Bill RM, Casanova S, Chen C-L, Conner M, Freger V, Gong B, Góra A, Hinds B et al..  2018.  Structure and function of natural proteins for water transport: general discussion.. Faraday Discuss. 209:83-95.
Tran L, Basdevant N, Prévost C, Ha-Duong T.  2016.  Structure of ring-shaped Aβ42 oligomers determined by conformational selection. Sci. Rep.. 6:21429.
Prentiss M, Prévost C, Danilowicz C.  2015.  Structure/function relationships in RecA protein-mediated homology recognition and strand exchange. Crit. Rev. Biochem. Mol. Biol.. 50:453–76.
Chebaro Y, Mousseau N, Derreumaux P.  2009.  Structures and Thermodynamics of Alzheimer's Amyloid-beta A beta(16-35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length A beta Fibrillation. J. Phys. Chem. B. 113:7668–7675.
Derreumaux P, Dauchez M, VERGOTEN G.  1993.  THE STRUCTURES AND VIBRATIONAL FREQUENCIES OF A SERIES OF ALKANES USING THE SPASIBA FORCE-FIELD. J. Mol. Struct.. 295:203–221.
Chebaro Y, Jiang P, Zang T, Mu Y, Nguyen PH, Mousseau N, Derreumaux P.  2012.  Structures of A beta 17-42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure. J. Phys. Chem. B. 116:8412–8422.
Melquiond A, Mousseau N, Derreumaux P.  2006.  Structures of soluble amyloid oligomers from computer simulations. Proteins: Struct., Funct., Bioinf.. 65:180–191.
Tarus B, Tran T-T, Nasica-Labouze J, Sterpone F, Nguyen PH, Derreumaux P.  2015.  Structures of the Alzheimer’s Wild-Type A beta 1-40 Dimer from Atomistic Simulations. J. Phys. Chem. B. 119:10478–10487.
Solovjeva T.F, Naberezhnykh G.A, Mazur AK, Khomenko V.A, Ovodov Y.S.  1986.  A study of interaction of an O-specific polysaccharide from Pseudomonas fluorescense with antibodies. Bioorg. Chem.. 12:265–272.
Peoc'h K, Levavasseur E, Delmont E, Laffont-Proust ADe Simone, Privat N, Chebaro Y, Bedoucha CChapuis Pi, Brandel J-P, Laquerriere A, Hauw J-LKemeny Jea et al..  2012.  Substitutions at residue 211 in the prion protein drive a switch between CJD and GSS syndrome, a new mechanism governing inherited neurodegenerative disorders. Hum. Mol. Genet.. 21:5417–5428.
Mazur AK.  1999.  Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion. J. Chem. Phys.. 111:1407–1414.
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Cubellis M.V, Baaden M., Andreotti G..  2015.  Taming molecular flexibility to tackle rare diseases. Biochimie. 113:54–58.
Timsit Y, Bombard S..  2007.  The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction. Rna. 13:2098–2107.
Taly A, Baciou L., Sebban P..  2002.  The DMPC lipid phase transition influences differently the first and the second electron transfer reactions in bacterial reaction centers. Febs Lett.. 532:91–96.
Zhang Y., Baaden M., Yan J., Shao J., Qiu S., Wu Y., Ding Y..  2010.  The molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor Tom20 from Oryza sativa involves an LRTLA motif. J. Phys. Chem. B. 114:13839–13846.
Nawrocki W.J, Tourasse N.J, Taly A, Rappaport F., Wollman F.A.  2015.  The plastid terminal oxidase: its elusive function points to multiple contributions to plastid physiology. Annu. Rev. Plant Biol.. 66:49–74.
Oteri F, Ciaccafava A, Poulpiquet A, Baaden M, Lojou E, Sacquin-Mora S.  2014.  The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes. Phys. Chem. Chem. Phys.. 16:11318–11322.
Stadler A.M, Garvey C.J, Bocahut A., Sacquin-Mora S, Digel I., Schneider G.J, Natali F., Artmann G.M, Zaccai G..  2012.  Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics. J. R. Soc. Interface. 9:2845–2855.
Perez S., Tubiana T., Imberty A., Baaden M..  2015.  Three-dimensional representations of complex carbohydrates and polysaccharides–SweetUnityMol: a video game-based computer graphic software. Glycobiology. 25:483–491.
Jiang R., Taly A, Lemoine D., Martz A., Cunrath O., Grutter T..  2012.  Tightening of the ATP-binding sites induces the opening of P2X receptor channels. Embo J.. 31:2134–2143.
Beedle AEM, Mora M, Lynham S, Stirnemann G, Garcia-Manyes S.  2017.  Tailoring protein nanomechanics with chemical reactivity. Nat Commun. 8:15658.
Chebaro Y, Derreumaux P.  2009.  Targeting the early steps of A beta 16-22 protofibril disassembly by N-methylated inhibitors: A numerical study. Proteins: Struct., Funct., Bioinf.. 75:442–452.
Derreumaux P, Man VHoang, Wang J, Nguyen PHoang.  2020.  Tau R3-R4 Domain Dimer of the Wild Type and Phosphorylated Ser356 Sequences. I. In Solution by Atomistic Simulations.. J Phys Chem B.

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