Publications

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C
Katava M, Stirnemann G, Zanatta M, Capaccioli S, Pachetti M, Ngai KL, Sterpone F, Paciaroni A.  2017.  Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion. Proc Natl Acad Sci U S A. 114:9361-9366.
D
Konstantakaki M., Changeux J-P, Taly A.  2007.  Docking of alpha-cobratoxin suggests a basal conformation of the nicotinic receptor. Biochem. Biophys. Res. Commun.. 359:413–418.
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.
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Brannigan G, Hénin J, Law R, Eckenhoff RG, Klein ML.  2008.  Embedded cholesterol in the nicotinic acetylcholine receptor. Proc. Natl. Acad. Sci. U.s.a.. 105:14418–14423.
Kynast P, Derreumaux P, Strodel B.  2016.  Evaluation of the coarse-grained OPEP force field for protein-protein docking. Bmc Biophysics. 9
Hénin J, Fiorin G, Chipot C, Klein ML.  2010.  Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. J. Chem. Theory Comput.. 6:35–47.
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Sommer B, Baaden M, Krone M, Woods A.  2018.  From Virtual Reality to Immersive Analytics in Bioinformatics.. J Integr Bioinform. 15(2)
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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.
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.
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.
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Barboiu M, Kumar M, Baaden M, Gale PA, Hinds BJ.  2019.  Highlights from the Faraday Discussion on Artificial Water Channels, Glasgow, UK.. Chem Commun (Camb). 55(27):3853-3858.
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.
Stirnemann G, Kang S-gu, Zhou R, Berne BJ.  2014.  How force unfolding differs from chemical denaturation.. Proc. Natl. Acad. Sci. U.s.a. 111:3413–8.
Spichty M, Taly A, Hagn F, Kessler H, Barluenga S, Winssinger N, Karplus M.  2009.  The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15 N chemical shifts. Biophys. Chem.. 143:111–123.
Spichty M, Taly A, Hagn F, Kessler H, Barluenga S, Winssinger N, Karplus M.  2009.  The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15 N chemical shifts. Biophys. Chem.. 143:111–123.
Kamashev D, Balandina A, Mazur AK, Arimondo PB, Rouviere-Yan, iv J.  2008.  HU binds and folds single-stranded DNA. Nucl. Acids Res.. 36:1026–1036.
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Taly A, Corringer P.J, Grutter T., L. de Carvalho P, Karplus M., Changeux J-P.  2006.  Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors. Proc. Natl. Acad. Sci. U.s.a.. 103:16965–16970.
Taly A, Corringer P-J, Grutter T, De Carvalho LPrado, Karplus M, Changeux J-P.  2006.  Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors. Proceedings of the National Academy of Sciences. 103:16965–16970.
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.
Kobus M, Nguyen PHoang, Stock G.  2010.  Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study. J. Chem. Phys.. 133
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.
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.
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.
Brovchenko I, Krukau A, Oleinikova A, Mazur AK.  2008.  Ion dynamics and water percolation effects in DNA polymorphism. J. Am. Chem. Soc.. 130:121–131.
K
Gracy J, Le-Nguyen D, Gelly J-C, Kaas Q, Heitz A, Chiche L.  2008.  KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007. Nucleic Acids Res.. 36:D314-D319.

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