Publications

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Perez S., Tubiana T., Imberty A., Baaden M.  2015.  Three-dimensional representations of complex carbohydrates and polysaccharides–SweetUnityMol: a video game-based computer graphic software. Glycobiology. 25:483–491.
Perales-Calvo J, Giganti D, Stirnemann G, Garcia-Manyes S.  2018.  The force-dependent mechanism of DnaK-mediated mechanical folding. Sci Adv. 4:eaaq0243.
Peoc'h K, Levavasseur E, Delmont E, Laffont-Proust ADe Simone, Privat N, Chebaro Y, Bedoucha CChapuis Pi, Brandel J-P, Laquerriere A, Hauw J-LKemeny Jea et al..  2012.  Substitutions at residue 211 in the prion protein drive a switch between CJD and GSS syndrome, a new mechanism governing inherited neurodegenerative disorders. Hum. Mol. Genet.. 21:5417–5428.
Pasquali S., Gan H.H., Schlick T..  2005.  Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs. Nuc. Acids Res.. 33:1384–1398.
Pasquali S, Derreumaux P.  2010.  HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA. J. Phys. Chem. B. 114:11957–11966.
Pasquali S., Maggs A.C..  2009.  Numerical studies of Lifshitz interactions between dielectrics. Phys. Rev. A. 79:020102(R).
Pasquali S., Maggs A.C..  2008.  Fluctuation-induced interactions between dielectrics. J. Chem. Phys.. 129:014703.
Pasquali S., Nitti F., Maggs A.C..  2008.  Numerical methods for fluctuation driven interactions between dielectrics. Phys. Rev. E. 77:016705.
Pasquali S., Percus J.K..  2006.  Mapping a Homopolymer onto a Model Fluid. J. Chem. Phys.. 125:064906.
Pasquali S., Percus J.K.  2009.  Mean field and the confined single homopolymer. Mol. Phys.. 107:1303–1312.
Parton D.L, Tek A., Baaden M, Sansom M.S.  2013.  Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations. Plos Comput. Biol.. 9:e1003034.
Parody-Morreale A, Robert CH, Bishop GA, Gill SJ.  1987.  Calorimetric studies of oxygen and carbon monoxide binding to human hemoglobin. Sequential binding heats for oxygen. J. Biol. Chem.. 262:10994–10999.
Parody-Morreale A., Robert C.H, Gill S.J.  1987.  Calorimetric analysis of oxygen binding to lobster hemocyanin. Invertebrate Oxygen Carriers.
Park S-M, Nguyen PHoang, Stock G.  2009.  Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent. J. Chem. Phys.. 131
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Oteri F, Ciaccafava A, Poulpiquet A, Baaden M, Lojou E, Sacquin-Mora S.  2014.  The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes. Phys. Chem. Chem. Phys.. 16:11318–11322.
Oteri F, Baaden M, Lojou E, Sacquin-Mora S.  2014.  Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans. J. Phys. Chem. B. 118:13800–13811.
Oleinikova A, Brovchenko I, Krukau A, Mazur AK.  2008.  Anomalous diffusion of ions at the surface of hydrated DNA molecule. Europhys. Lett.. 82:46002.
O'Donnell T, Robert CH, Cazals F.  2022.  Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions. Proteins: Structure, Function, and Bioinformatics. 90:858-868.
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Nury H., Poitevin F., Van Renterghem C., Changeux J.P, Corringer P.J, Delarue M., Baaden M.  2010.  One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proc. Natl. Acad. Sci. U.s.a.. 107:6275–6280.
Nury H., Van Renterghem C., Weng Y., Tran A., Baaden M, Dufresne V., Changeux J.-P., Sonner J.M, Delarue M., Corringer P.-J..  2011.  X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Nature. 469:428–431.
Nissen LJ, Gelly JC, Hipskind RA.  2001.  Induction-independent recruitment of CREB-binding protein to the c-fos serum response element through interactions between the bromodomain and Elk-1. J. Biol. Chem.. 276:5213–5221.
Nishikawa N., Nguyen PHoang, Derreumaux P, Okamoto Y..  2013.  Replica-exchange molecular dynamics simulations of the amyloid-beta(16-22) fragments. European Biophysics Journal with Biophysics Letters. 42:S68.
Nishikawa N, Nguyen PHoang, Derreumaux P, Okamoto Y.  2015.  Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation. Mol. Simul.. 41:1041–1044.
Nguyent P, Derreumaux P.  2014.  Understanding Amyloid Fibril Nucleation and A beta Oligomer/Drug Interactions from Computer Simulations. Acc. Chem. Res.. 47:603–611.
Nguyen PHoang.  2006.  Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis. Proteins: Struct., Funct., Bioinf.. 65:898–913.

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