Publications

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Baaden M, Berny F, Wipff G.  2001.  The chloroform TBP aqueous nitric acid interfacial system: a molecular dynamics investigation. J. Mol. Liq.. 90:1–9.
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.
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.
Migliore M, Bonvicini A, Tognetti V, Guilhaudis L, Baaden M, Oulyadi H, Joubert L, Ségalas-Milazzo I.  2020.  Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study.. Phys Chem Chem Phys. 22(3):1611-1623.
Nasica-Labouze J, Meli M, Derreumaux P, Colombo G, Mousseau N.  2011.  Characterization of the Aggregation Pathway for a 20-mer of GNNQQNY using Coarse-Grained and All-Atom Representations. Biophys. J.. 100:BiophysSoc.
Loriot S, Sachdeva S, Bastard K, Prévost C, Cazals F.  2011.  On the characterization and selection of diverse conformational ensembles with applications to flexible docking. Ieee/acm Trans. Comput. Biol. Bioinform.. 8:487–98.
Chakravarty D, Janin J, Robert CH, Chakrabarti P.  2015.  Changes in protein structure at the interface accompanying complex formation.. Iucrj. 2:643–652.
Gerencser L, Taly A, Baciou L, Maroti P, Sebban P.  2002.  Cd2+ binding effect on bacterial reaction center mutants: The proton penetration involves interdependent pathways. BIOPHYSICAL JOURNAL. 82:518A-518A.
Baaden M, Wipff G, Yaftian MR, Burgard M, Matt D.  2000.  Cation coordination by calix[4]arenes bearing amide and/or phosphine oxide pendant groups: how many arms are needed to bind Li+ vs. Na+? A combined NMR and molecular dynamics study Journal of the Chemical Society-perkin Transactions 2. :1315–1321.
Mazur AK, Haser R., Payan F..  1994.  The catalytic mechanism of {$\alpha$}-amylases based upon enzyme crystal structures and model building calculations. Biochem. Biophys. Res. Commun.. 204:297–302.
Li H, Luo Y, Derreumaux P, Wei G.  2011.  Carbon Nanotube Inhibits the Formation of beta-Sheet-Rich Oligomers of the Alzheimer’s Amyloid-beta(16-22) Peptide. Biophys. J.. 101:2267–2276.
Doyle ML, Di Cera E, Robert CH, Gill SJ.  1987.  Carbon dioxide and oxygen linkage in human hemoglobin tetramers. J. Mol. Biol.. 196:927–934.
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.
Lambert B, Jacques V, Shivanyuk A, Matthews SE, Tunayar A, Baaden M, Wipff G, Bohmer V, Desreux JF.  2000.  Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes. Inorg. Chem.. 39:2033–2041.
Timsit Y, Moras D..  1992.  Crystallization of DNA. Meth. Enzymol.. 211:409–429.
Timsit Y, Moras D..  1996.  Cruciform structures and functions. Q. Rev. Biophys.. 29:279–307.
Timsit Y.  2001.  Convergent evolution of MutS and topoisomerase II for clamping DNA crossovers and stacked Holliday junctions. J. Biomol. Struct. Dyn.. 19:215–218.
Delalande O., Ferey N., Grasseau G., Baaden M..  2009.  Complex molecular assemblies at hand via interactive simulations. J. Comput. Chem.. 30:2375–2387.
Guerlet G., Taly A, L. de Carvalho P, 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.
Timsit Y, Allemand F., Chiaruttini C., Springer M..  2006.  Coexistence of two protein folding states in the crystal structure of ribosomal protein L20. Embo Rep.. 7:1013–1018.
Durrieu M.P, Bond P.J, Sansom M.S, Lavery R., Baaden M..  2009.  Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states. Chemphyschem. 10:1548–1552.
Baaden M., Marrink S.J.  2013.  Coarse-grain modelling of protein-protein interactions. Curr. Opin. Struct. Biol.. 23:878–886.
Francia F., Malferrari M., Sacquin-Mora S, Venturoli G..  2009.  Charge Recombination Kinetics and Protein Dynamics in Wild Type and Carotenoid-less Bacterial Reaction Centers: Studies in Trehalose Glasses. J. Phys. Chem. B. 113:10389–1398.

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