Publications

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2014
Kalimeri M, Girard E, Madern D, Sterpone F.  2014.  Interface Matters: The Stiffness Route to Stability of a Thermophilic Tetrameric Malate Dehydrogenase. Plos One. 9:e113895.
Sterpone F., Melchionna S., Tuffery P, Pasquali S., Mousseau N., Cragnolini T., Chebaro Y, St-Pierre J.-F., Kalimeri M., Barducci A. et al..  2014.  The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem. Soc. Rev.. 43:4871–4893.
2013
Bestaoui-Berrekhchi-Berrahma N, Derreumaux P, Sekkal-Rahal M, Springborg M, Sayede A, Yousfi N, Kadoun A-E-D.  2013.  Density functional conformational study of 2-O-sulfated 3,6 anhydro-alpha-D-galactose and of neo-kappa- and iota-carrabiose molecules in gas phase and water. J. Mol. Model.. 19:893–904.
Calimet N., Simoes M., Changeux J.P, Karplus M., Taly A, Cecchini M..  2013.  A gating mechanism of pentameric ligand-gated ion channels. Proc. Natl. Acad. Sci. U.s.a.. 110:E3987–3996.
Kalimeri M, Rahaman O, Melchionna S, Sterpone F.  2013.  How Conformational Flexibility Stabilizes the Hyperthermophilic Elongation Factor G-Domain. J. Phys. Chem. B. 117:13775–13785.
Sterpone F, Nguyen PHoang, Kalimeri M, Derreumaux P.  2013.  Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation. J. Chem. Theory Comput.. 9:4574–4584.
Kalimeri M, Melchionna S, Sterpone F.  2013.  Inquiring Protein Thermostability: Is Resistance to Temperature Stress a Rigidity/Flexibility Trade-off? Proceedings of the European Conference on Complex Systems 2012.
Sauguet L., Poitevin F., Murail S., Van Renterghem C., Moraga-Cid G., Malherbe L., Thompson A.W, Koehl P., Corringer P.J, Baaden M et al..  2013.  Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. Embo J.. 32:728–741.
Fiorin G, Klein ML, Hénin J.  2013.  Using collective variables to drive molecular dynamics simulations. Mol. Phys.. 111:3345–3362.
2012
Tek A., Laurent B., Piuzzi M., Lu Z., Baaden M, Delalande O., Chavent M, Férey N, Martin C., Piccinali L. et al..  2012.  Advances in Human-Protein Interaction - Interactive And Immersive Molecular Simulations.
LeBard DN, Hénin J, Eckenhoff RG, Klein ML, Brannigan G.  2012.  General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity. Plos Comput. Biol.. 8:e1002532.
Lörinczi É, Bhargava Y, Marino SF, Taly A, Kaczmarek-Hájek K, Barrantes-Freer A, Dutertre S, Grutter T, Rettinger J, Nicke A.  2012.  Involvement of the cysteine-rich head domain in activation and desensitization of the P2X1 receptor. Proceedings of the National Academy of Sciences of the United States of America. 109:11396–11401.
2011
Kobus M, Nguyen PHoang, Stock G.  2011.  Coherent vibrational energy transfer along a peptide helix. J. Chem. Phys.. 134
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.
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.
Chavent M, Lévy B., Krone M., Bidmon K., Nominé J.P, Ertl T., Baaden M.  2011.  GPU-powered tools boost molecular visualization. Briefings Bioinf.. 12:689–701.
Kamashev D, Oberto J, Serebryakova M, Gorbachev A, Zhukova Y, Levitsk, ii S, Mazur AK, Govorun V.  2011.  Mycoplasma gallisepticum produces a histone-like protein that recognizes base mismatches in DNA. Biochemistry. 50:8692–8702.
Kobus M, Lieder M, Nguyen PHoang, Stock G.  2011.  Simulation of transient infrared spectra of a photoswitchable peptide. J. Chem. Phys.. 135
2010
Hénin J, Brannigan G, Dailey WP, Eckenhoff RG, Klein ML.  2010.  An atomistic model for simulations of the general anesthetic isoflurane. J. Phys. Chem. B. 114:604–612.

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