Publications

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Book Chapter
Stock G., Jain A., Riccardi L., Nguyen PHoang.  2011.  Exploring the energy landscape of small peptides and proteins by molecular dynamics simulations.
Conference Paper
Krieger E., Leger L., Durrieu M.P., Taib N., Bond P., Laguerre M., Lavery R., Sansom M.S.P., Baaden M.  2007.  Atomistic modeling of the membrane-embedded synaptic fusion complex: a grand challenge project on the DEISA HPC infrastructure. ParCo 2007, Parallel Computing: Architectures, Algorithms and Applications. 38:729–736.
Journal Article
Lu Y, Shi X-F, Nguyen PHoang, Sterpone F, Jr FRSalsbury, Derreumaux P.  2019.  Amyloid-β (29–42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids. The Journal of Physical Chemistry B. 123:2687–2696.
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.
Connelly PR, Johnson CR, Robert CH, Bak HJ, Gill SJ.  1989.  Binding of oxygen and carbon monoxide to the hemocyanin from the spiny lobster. J. Mol. Biol.. 207:829–832.
Guerlet G., Taly A, L. de Carvalho P, Martz A., Jiang R., Specht A., Le Novere N., Grutter T..  2008.  Comparative models of P2X2 receptor support inter-subunit ATP-binding sites. Biochem. Biophys. Res. Commun.. 375:405–409.
Lambert B, Jacques V, Shivanyuk A, Matthews SE, Tunayar A, Baaden M, Wipff G, Bohmer V, Desreux JF.  2000.  Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes. Inorg. Chem.. 39:2033–2041.
Chakravarty D, Janin J, Robert CH, Chakrabarti P.  2015.  Changes in protein structure at the interface accompanying complex formation.. Iucrj. 2:643–652.
Migliore M, Bonvicini A, Tognetti V, Guilhaudis L, Baaden M, Oulyadi H, Joubert L, Ségalas-Milazzo I.  2020.  Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study.. Phys Chem Chem Phys. 22(3):1611-1623.
Johnson CN, Adkins NL, Georgel P.  2005.  Chromatin remodeling complexes: ATP-dependent machines in action.. Biochem. Cell Biol.. 83:405–417.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Guerlet G, Taly A, De Carvalho LPrado, Martz A, Jiang R, Specht A, Le Novere N, Grutter T.  2008.  Comparative models of P2X2 receptor support inter-subunit ATP-binding sites. Biochem. Biophys. Res. Commun.. 375:405–409.
Puyo-Fourtine J, Juillé M, Hénin J, Clavaguéra C, Duboué-Dijon E.  2022.  Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J. Phys. Chem. B. 126(22):4022-4034.
Taly A, Colas C., Malliavin T., Blondel A., Nilges M., Corringer P.J, Joseph D..  2011.  Discrimination of agonists versus antagonists of nicotinic ligands based on docking onto AChBP structures. J. Mol. Graph. Model.. 30:100–109.
Sikorav J.L., Duplantier B., Jannink G., Timsit Y.  1998.  DNA crossovers and type II DNA topoisomerases: A thermodynamical study. J. Mol. Biol.. 284:1279–1287.
Man VHoang, He X, Derreumaux P, Ji B, Xie X-Q, Nguyen PHoang, Wang J.  2019.  Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: the case of aβ16–22 dimer. Journal of chemical theory and computation. 15:1440–1452.
Jaiteh M, Taly A, Hénin J.  2016.  Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors.. Plos One. 11:e0151934.
Jiang R., Lemoine D., Martz A., Taly A, Gonin S., L. de Carvalho P, Specht A., Grutter T..  2011.  Agonist trapped in ATP-binding sites of the P2X2 receptor. Proc. Natl. Acad. Sci. U.s.a.. 108:9066–9071.
Qiu Y, Zhao Y, Becker M, John S, Parekh BS, Huang S, Hendarwanto A, Martinez ED, Chen Y, Lu H et al..  2006.  HDAC1 acetylation is linked to progressive modulation of steroid receptor-induced gene transcription.. Mol. Cell. 22:669–679.
Jiang R., Taly A, Lemoine D., Martz A., Specht A., Grutter T..  2012.  Intermediate closed channel state(s) precede(s) activation in the ATP-gated P2X2 receptor. Channels (austin). 6:398–402.
Lemoine D, Jiang R, Taly A, Chataigneau T, Specht A, Grutter T.  2012.  Ligand-gated ion channels: new insights into neurological disorders and ligand recognition. Chem. Rev.. 112:6285–6318.
Jiang R., Taly A, Grutter T..  2013.  Moving through the gate in ATP-activated P2X receptors. Trends Biochem. Sci.. 38:20–29.
Stirnemann G, Wernersson E, Jungwirth P, Laage D.  2013.  Mechanisms of acceleration and retardation of water dynamics by ions. J. Am. Chem. Soc.. 135:11824–11831.

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