Publications

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C
Lee S, Tran A, Allsopp M, Lim JB, Hénin J, Klauda JB.  2014.  CHARMM36 united atom chain model for lipids and surfactants.. J. Phys. Chem. B. 118:547–556.
Grutter T., L. de Carvalho P, Virginie D., Taly A, Fischer M., Changeux J-P.  2005.  A chimera encoding the fusion of an acetylcholine-binding protein to an ion channel is stabilized in a state close to the desensitized form of ligand-gated ion channels. C. R. Biol.. 328:223–234.
Chiricotto M., Tran T-T, Nguyen PHoang, Melchionna S., Sterpone F, Derreumaux P.  2016.  Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation. Isr. J. Chem.. DOI: 10.1002/ijch.201600048.
Maupetit J, Tuffery P, Derreumaux P.  2007.  A coarse-grained protein force field for folding and structure prediction. Proteins: Struct., Funct., Bioinf.. 69:394–408.
Berthoumieu O, Nguyen PHoang, del Castillo-Frias MP, Ferre S, Tarus B, Nasica-Labouze J, Noel S, Saurel O, Rampon C, Doig AJ et al..  2015.  Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp. Chemistry-a European Journal. 21:12657–12666.
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.
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.
Troxler L, Baaden M, Bohmer V, Wipff G.  2000.  Complexation of M3+ lanthanide cations by calix[4]arene-CMPO ligands: A molecular dynamics study in methanol solution and at a water/chloroform interface. Supramol. Chem.. 12:27+.
Catharina L, Lima CRibeiro, Franca A, Guimarães ACarolina R, Alves-Ferreira M, Tuffery P, Derreumaux P, Carels N.  2017.  A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against.. Bioinform Biol Insights. 11:1177932217712471.
Bou-Nader C, Pecqueur L, Barraud P, Fontecave M, Tisné C, Sacquin-Mora S, Hamdane D.  2019.  Conformational Stability Adaptation of a Double-Stranded RNA-Binding Domain to Transfer RNA Ligand.. Biochemistry. 58(20):2463-2473.
Smith JC, Cournia Z, Taly A, Tournier AL, Mihailescu D, G Ullmann M.  2004.  Conformational transitions in proteins and membranes. Novel Approaches to the Structure and Dynamics of Liquids: Experiments, Theories and Simulations. :485–502.
Smith JC, Cournia Z, Taly A, Tournier AL, Mihailescu D, G Ullmann M.  2004.  Conformational transitions in proteins and membranes. Novel Approaches to the Structure and Dynamics of Liquids: Experiments, Theories and Simulations. :485–502.
Trellet M., Férey N, Baaden M, Bourdot P..  2015.  Content and task based navigation for structural biology in 3D environments. Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on. :31–36.
Trellet M., Férey N, Baaden M, Bourdot P..  2014.  Content-guided Navigation in Multimeric Molecular Complexes. {BIOIMAGING} 2014 - Proceedings of the International Conference on Bioimaging, ESEO, Angers, Loire Valley, France, 3-6 March, 2014. :76–81.
Pons S, Sallette J, Bourgeois JP, Taly A, Changeux J-P, Devillers-Thiéry A.  2004.  Critical role of the C-terminal segment in the maturation and export to the cell surface of the homopentameric $\alpha$7–5HT3A receptor. Eur. J. Neurosci.. 20:2022–2030.
Tung NThanh, Derreumaux P, Vu VV, Nam PCam, Ngo STung.  2019.  C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ Tetramer in Solution: Intensive MD Study.. ACS Omega. 4(6):11066-11073.
D
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.
Timsit Y, Moras D..  1994.  DNA self-fitting: the double helix directs the geometry of its supramolecular assembly. Embo J.. 13:2737–2746.
Timsit Y.  1999.  DNA structure and polymerase fidelity. J. Mol. Biol.. 293:835–853.
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.
Prévost C, Takahashi M., Lavery R.  2009.  Deforming DNA: from physics to biology. Chemphyschem. 10:1399–404.

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