Publications

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2010
Heddi B., Oguey C., Lavelle C., Foloppe N., Hartmann B..  2010.  Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res.. 38:1034–1047.
Tek A, Laurent B, Férey N, Baaden M.  2010.  Interacting with Molecular Simulations using a Multimodal VR Framework. EuroVR-EVE. :1–4.
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.
Brannigan G, LeBard DN, Hénin J, Eckenhoff RG, Klein ML.  2010.  Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain.. Proc. Natl. Acad. Sci. U.s.a.. 107:14122–14127.
Sinha D.K, Neveu P., Gagey N., Aujard I., Benbrahim-Bouzidi C., Le Saux T., Rampon C., Gauron C., Goetz B., Dubruille S. et al..  2010.  Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination. Chembiochem. 11:653–663.
Chavent M, Vanel A., Lévy B., Raffin B., Tek A., Baaden M.  2010.  A Rendering Method for Small Molecules up to Macromolecular Systems: HyperBalls Accelerated by Graphics Processors. JOBIM.
Heddi B., Abi-Ghanem J., Lavigne M., Hartmann B..  2010.  Sequence-dependent DNA flexibility mediates DNase I cleavage. J. Mol. Biol.. 395:123–133.
Valleix S., Derreumaux P, Garnier C., Briki F., Boimard M., Doucet J., Rioux-Leclercq N., Martin L., Grateau G., Delpech M. et al..  2010.  The VLITL aggregation-prone motif might trigger amyloid fibril formation of fibrinogen A alpha-chain frameshift variants in vivo. Amyloid-journal of Protein Folding Disorders. 17:96–97.
Stirnemann G, Hynes JT, Laage D.  2010.  Water hydrogen bond dynamics in aqueous solutions of amphiphiles. J. Phys. Chem. B. 114:3052–3059.
Sterpone F, Stirnemann G, Hynes JT, Laage D.  2010.  Water hydrogen-bond dynamics around amino acids: the key role of hydrophilic hydrogen-bond acceptor groups. J. Phys. Chem. B. 114:2083–9.
Stirnemann G, Rossky PJ, Hynes JT, Laage D.  2010.  Water reorientation, hydrogen-bond dynamics and 2D-IR spectroscopy next to an extended hydrophobic surface.. Farad. Discuss.. 146:263–281.
2011
Li H, Luo Y, Derreumaux P, Wei G.  2011.  Carbon Nanotube Inhibits the Formation of beta-Sheet-Rich Oligomers of the Alzheimer’s Amyloid-beta(16-22) Peptide. Biophys. J.. 101:2267–2276.
Li H, Luo Y, Derreumaux P, Wei G.  2011.  Carbon Nanotube Inhibits the Formation of beta-Sheet-Rich Oligomers of the Alzheimer’s Amyloid-beta(16-22) Peptide. Biophys. J.. 101:2267–2276.
Loriot S, Sachdeva S, Bastard K, Prévost C, Cazals F.  2011.  On the characterization and selection of diverse conformational ensembles with applications to flexible docking. Ieee/acm Trans. Comput. Biol. Bioinform.. 8:487–98.
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.
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.
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.
Stirnemann G, Sterpone F, Laage D.  2011.  Dynamics of water in concentrated solutions of amphiphiles: Key roles of local structure and aggregation. J. Phys. Chem. B. 115:3254–3262.
Nguyen PHoang, Li MSuan, Derreumaux P.  2011.  Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer. Phys. Chem. Chem. Phys.. 13:9778–9788.
Lu Y, Wei G, Derreumaux P.  2011.  Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-beta Fragment 29-42 by Replica Exchange Molecular Dynamics Simulations. J. Phys. Chem. B. 115:1282–1288.
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.

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