Publications

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Férey N, Gros P.-E., Hérisson J., Gherbi R..  2004.  A Distributed Multimedia Database Visualization within An Immersive Environment for Bioinformatics. International Symposium on Multimedia Software Engineering (ISMSE 2004 - IEEE). :156–159.
Prévost C, Boudvillain M, Beudaert P, Leng M, Lavery R, Vovelle F.  1997.  Distortions of the DNA double helix induced by 1,3-trans-diamminedichloroplatinum(II)-intrastrand cross-link: An internal coordinate molecular modeling study. J. Biomol. Struct. Dyn.. 14:703–714.
Cote S, Derreumaux P, Mousseau N.  2011.  Distinct Morphologies for Amyloid Beta Protein Monomer: A beta(1-40), A beta(1-42), and A beta(1-40)(D23N). J. Chem. Theory Comput.. 7:2584–2592.
Cote S, Laghaei R, Derreumaux P, Mousseau N.  2012.  Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: A beta(1-40), A beta(1-42), and A beta(1-40)(D23N). J. Phys. Chem. B. 116:4043–4055.
Sterpone F, Spanu L, Ferraro L, Sorella S, Guidoni L.  2008.  Dissecting the Hydrogen Bond: A Quantum Monte Carlo Approach. J Chem Theo Comp. 4:1428–1434.
Mazur AK, Nguyen T-S, Gladyshev E.  2020.  Direct Homologous dsDNA-dsDNA Pairing: How, Where, and Why? J Mol Biol. 432(3):737-744.
Stirnemann G, Laage D.  2010.  Direct evidence of angular jumps during water reorientation through two-dimensional infrared anisotropy. J. Phys. Chem. Lett.. 1:1511–1516.
Phuong NH, Germano G, Schmid F.  2002.  The direct correlation function in nematic liquid crystals from computer simulation. Comput. Phys. Commun.. 147:350–353.
Nguyen PHoang, Sterpone F, Pouplana R, Derreumaux P, Campanera JM.  2016.  Dimerization Mechanism of Alzheimer A beta(40) Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation. J. Phys. Chem. B. 120:12111–12126.
Altis A, Nguyen PHoang, Hegger R, Stock G.  2007.  Dihedral angle principal component analysis of molecular dynamics simulations. J. Chem. Phys.. 126
Derreumaux P.  1997.  A diffusion process-controlled Monte Carlo method for finding the global energy minimum of a polypeptide chain .1. Formulation and test on a hexadecapeptide. J. Chem. Phys.. 106:5260–5270.
Hénin J, Tajkhorshid E, Schulten K, Chipot C.  2008.  Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophys. J.. 94:832–839.
Georgel PT, Robert CH.  2002.  Differential core histone binding behavior: RNA polymerase I promoter region vs 5S rDNA positioning DNA sequences. Cell Biochem. Biophys.. 37:1–13.
Colloc'h N., Sacquin-Mora S, Avella G., Dhaussy A.C, Prange T., Vallone B., Girard E..  2017.  Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography. Sci Rep. 7:1858.
Alvarez J, Irrmann O, Djaouti D, Taly A, Rampnoux O, Sauvé L.  2019.  Design games and game design: Relations between design, codesign and serious games in adult education. From UXD to LivXD: Living eXperience Design. :229–253.
Spalvieri D, Mauviel A-M, Lambert M, Férey N, Sacquin-Mora S, Chavent M, Baaden M.  2022.  Design – a new way to look at old molecules. Journal of Integrative Bioinformatics. 19:20220020.
Mazur AK, Dorofeyev VE, Abagyan RA.  1991.  Derivation and testing of explicit equations of motion for polymers described by internal coordinates. J. Comput. Phys.. 92:261–272.
Tuffery P, Derreumaux P.  2005.  Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm. Proteins: Struct., Funct., Bioinf.. 61:732–740.
Baaden M, Granger P, Strich A.  2000.  Dependence of NMR isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-X. Mol. Phys.. 98:329–342.
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.
Thevenet P., Shen Y., Maupetit J., Guyon F., Padilla A., Derreumaux P, Tuffery P.  2012.  Delivering the native structures of peptides from computer simulations and predicted NMR proton chemical shifts. J. Pept. Sci.. 18:S38.
Prévost C, Takahashi M., Lavery R.  2009.  Deforming DNA: from physics to biology. Chemphyschem. 10:1399–404.
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.
Abi-Ghanem J., Heddi B., Foloppe N., Hartmann B..  2010.  DNA structures from phosphate chemical shifts. Nucleic Acids Res.. 38:e18.
Timsit Y.  1999.  DNA structure and polymerase fidelity. J. Mol. Biol.. 293:835–853.

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