Publications

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Journal Article
Mondal J, Halverson D, Li ITS, Stirnemann G, Walker GC, Berne BJ.  2015.  How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory.. Proc. Natl. Acad. Sci. Usa. 112:9270–5.
Hénin J, Lopes LJS, Fiorin G.  2022.  Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD.. J Chem Theory Comput. 18(3):1945-1956.
Molza A.E, Férey N, Czjzek M, Le Rumeur E, Hubert J.F, Tek A, Laurent B, Baaden M, Delalande O..  2014.  Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly. Faraday Discuss.. 169:45–62.
Molza A.E, Férey N, Czjzek M, Le Rumeur E, Hubert J.F, Tek A, Laurent B, Baaden M, Delalande O..  2014.  Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly. Faraday Discuss.. 169:45–62.
Jiang R., Taly A, Lemoine D., Martz A., Specht A., Grutter T..  2012.  Intermediate closed channel state(s) precede(s) activation in the ATP-gated P2X2 receptor. Channels (austin). 6:398–402.
Heddi B., Oguey C., Lavelle C., Foloppe N., Hartmann B..  2010.  Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res.. 38:1034–1047.
Sacquin-Mora S, Carbone A., Lavery R.  2008.  Identification of Protein Interaction Partners and Protein-Protein Interaction Sites. J. Mol. Biol.. 382:1276–1289.
Bourassin N., Baaden M, Lojou E., Sacquin-Mora S.  2020.  Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation. J Phys Chem B. 124:8516–8523.
Lima CRibeiro, Carels N, Guimaraes ACarolina R, Tuffery P, Derreumaux P.  2016.  In silico structural characterization of protein targets for drug development against Trypanosoma cruzi. J. Mol. Model.. 22
Fu Z, Luo Y, Derreumaux P, Wei G.  2009.  Induced beta-Barrel Formation of the Alzheimer’s A beta 25-35 Oligomers on Carbon Nanotube Surfaces: Implication for Amyloid Fibril Inhibition. Biophys. J.. 97:1795–1803.
Fu Z, Luo Y, Derreumaux P, Wei G.  2009.  Induced beta-barrel formation of the Alzheimer's Abeta25-35 oligomers on carbon nanotube surfaces: implication for amyloid fibril inhibition.. Biophys. J.. 97:1795–1803.
Lu Y, Shi X-F, Salsbury FR, Derreumaux P.  2018.  Influence of electric field on the amyloid-β(29-42) peptides embedded in a membrane bilayer.. J Chem Phys. 148(4):045105.
Man VHoang, Li MSuan, Wang J, Derreumaux P, Nguyen PHoang.  2019.  Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level. The Journal of chemical physics. 150:215101.
Durrieu M-P, Lavery R, Baaden M.  2008.  Interactions between neuronal fusion proteins explored by molecular dynamics. Biophys. J.. 94:3436–3446.
Dreher M., Piuzzi M., Turki A., Chavent M, Baaden M, Férey N, Limet S., Raffin B., Robert S..  2013.  Interactive Molecular Dynamics: Scaling up to Large Systems.. Procedia Comput. Sci.. 18:20–29.
Sacquin-Mora S, Lavery R.  2006.  Investigating the local flexibility of functional residues in hemoproteins. Biophys. J.. 90:2706–2717.
Laurin Y., Savarin P., Robert CH, Takahashi M., Eyer J., Prévost C, Sacquin-Mora S.  2015.  Investigating the Structural Variability and Binding Modes of the Glioma Targeting NFL-TBS.40-63 Peptide on Tubulin. Biochemistry. 54:3660–3669.
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.
Mattei C, Taly A, Soualah Z, Saulais O, Henrion D, Guérineau NC, Verleye M, Legros C.  2019.  Involvement of the GABAA receptor α subunit in the mode of action of etifoxine. Pharmacological research. 145:104250.
Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A.  2009.  Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling. Plos Comput. Biol.. 5:e1000267.
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.
Gelly JC, Gracy J, Kaas Q, Le-Nguyen D, Heitz A, Chiche L.  2004.  The KNOTTIN website and database: a new information system dedicated to the knottin scaffold. Nucleic Acids Res.. 32:D156-D159.
Lemoine D, Jiang R, Taly A, Chataigneau T, Specht A, Grutter T.  2012.  Ligand-gated ion channels: new insights into neurological disorders and ligand recognition. Chem. Rev.. 112:6285–6318.
Sacquin-Mora S, Laforet E, Lavery R.  2007.  Locating the active sites of enzymes using mechanical properties. Proteins: Struct., Funct., Bioinf.. 67:350–359.
Sacquin-Mora S, Laforet E, Lavery R.  2007.  Locating the active sites of enzymes using mechanical properties. Proteins: Struct., Funct., Bioinf.. 67:350–359.

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