Publications

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Viet MHoang, Derreumaux P, Nguyen PHoang.  2015.  Communication: Multiple atomistic force fields in a single enhanced sampling simulation. J. Chem. Phys.. 143:021101.
Mazur AK.  1997.  Common molecular dynamics algorithms revisited: Accuracy and optimal time steps of St\H ormer-leapfrog integrators. J. Comput. Phys.. 136:354–365.
Mazur AK.  2013.  Comment on ’Length scale dependence of DNA mechanical properties’. Phys. Rev. Lett.. 111:179801.
Mazur AK.  2013.  Comment on ``Length Scale Dependence of DNA Mechanical Properties''. Phys. Rev. Lett.. 111
Gros P.-E., Hérisson J., Férey N, Gherbi R..  2004.  Combining Applications and Databases Integration Approaches in a Common Distributed Genomic Platform. International CODATA Conference, The Information Society: New Horizons for Science.
Stankowski S, Pawlak M, Kaisheva E, Robert CH, Schwarz G.  1991.  A combined study of aggregation, membrane affinity and pore activity of natural and modified melittin. Biochim. Biophys. Acta. 1069:77–86.
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.
Gabb H., Prévost C, Bertucat G., Robert CH, Lavery R.  1997.  Collective-variable Monte Carlo simulation of DNA. J. Comp. Chem.. 18:2001–2011.
Kobus M, Nguyen PHoang, Stock G.  2011.  Coherent vibrational energy transfer along a peptide helix. J. Chem. Phys.. 134
Sterpone F, Martinazzo R., Panda A.N., Burghardt I..  2011.  Coherent Excitation Transfer Driven by Torsional Dynamics: a Model Hamiltonian for PPV Type Systems. Zeitschrift Für Physikalische Chemie. 255:541–551.
Lavery R, Sacquin-Mora S.  2009.  Coarse-graining protein mechanics. Coarse-Graining of Condensed Phase and Biomolecular Systems
Cragnolini T, Derreumaux P, Pasquali S.  2013.  Coarse-Grained Simulations of RNA and DNA Duplexes. J. Phys. Chem. B. 117:8047–8060.
Stadlbauer P, Mazzanti L, Cragnolini T, Wales DJ, Derreumaux P, Pasquali S, Sponer J.  2016.  Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. J. Chem. Theory Comput.. 12:6077–6097.
Derreumaux P, Mousseau N.  2007.  Coarse-grained protein molecular dynamics simulations. J. Chem. Phys.. 126:025101.
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.
Chebaro Y, Pasquali S, Derreumaux P.  2012.  The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins. J. Phys. Chem. B. 116:8741–8752.
Derreumaux P.  2013.  coarse-grained models for protein folding ang aggregation. Methods Mol. Biol.. 924:585–600.
Cragnolini T, Laurin Y, Derreumaux P, Pasquali S.  2015.  Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings. J. Chem. Theory Comput.. 11:3510–3522.
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.
Sacquin-Mora S.  2019.  Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.. J R Soc Interface. 16(156):20190075.
Cragnolini T, Laurin Y, Derreumaux P, Pasquali S.  2014.  Coarse-Grain RNA Folding: Towards More Complex Structures. Biophys. J.. 106:283A.
Sacquin-Mora S.  2011.  Coarse-grain models for proteins: Mechanical properties and interactions.
Johnson CN, Adkins NL, Georgel P.  2005.  Chromatin remodeling complexes: ATP-dependent machines in action.. Biochem. Cell Biol.. 83:405–417.
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.

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