Publications

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Journal Article
Derreumaux P.  2013.  coarse-grained models for protein folding ang aggregation. Methods Mol. Biol.. 924:585–600.
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.
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.
Derreumaux P, Mousseau N.  2007.  Coarse-grained protein molecular dynamics simulations. J. Chem. Phys.. 126:025101.
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.
Cragnolini T, Derreumaux P, Pasquali S.  2013.  Coarse-Grained Simulations of RNA and DNA Duplexes. J. Phys. Chem. B. 117:8047–8060.
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.
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.
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.
Viet MHoang, Derreumaux P, Nguyen PHoang.  2015.  Communication: Multiple atomistic force fields in a single enhanced sampling simulation.. The Journal of Chemical Physics. 143:021101–021101.
Viet MHoang, Derreumaux P, Nguyen PHoang.  2015.  Communication: Multiple atomistic force fields in a single enhanced sampling simulation. J. Chem. Phys.. 143:021101.
Nguyen PHoang, Okamoto Y, Derreumaux P.  2013.  Communication: Simulated tempering with fast on-the-fly weight determination. J. Chem. Phys.. 138:061102.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Guerlet G, Taly A, De Carvalho LPrado, 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.
Derreumaux P, LAGANT P, VERGOTEN G.  1993.  COMPARISON OF THE IR AND RAMAN VIBRATIONAL FREQUENCIES AND INTENSITIES OF ALKANES USING THE AMBER AND SPASIBA FORCE-FIELDS - APPLICATION TO ETHANE, AND GAUCHE-N-BUTANE AND TRANS-N-BUTANE. J. Mol. Struct.. 295:223–232.
Wei GH, Mousseau N, Derreumaux P.  2004.  Complex folding pathways in a simple beta-hairpin. Proteins: Struct., Funct., Bioinf.. 56:464–474.
St-Pierre J-F, Mousseau N, Derreumaux P.  2008.  The complex folding pathways of protein A suggest a multiple-funnelled energy landscape. J. Chem. Phys.. 128:045101.
Catharina L, Lima CRibeiro, Franca A, Guimarães ACarolina R, Alves-Ferreira M, Tuffery P, Derreumaux P, Carels N.  2017.  A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against.. Bioinform Biol Insights. 11:1177932217712471.
Wei G, Mousseau N, Derreumaux P.  2007.  Computational Simulations of the Early Steps of Protein Aggregation. Prion. 1:3–8.
Forcellino F, Derreumaux P.  2001.  Computer simulations aimed at structure prediction of supersecondary motifs in proteins. Proteins-structure Function and Genetics. 45:159–166.
Nguyen PHoang, Derreumaux P.  2012.  Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature. Phys. Chem. Chem. Phys.. 14:877–886.
Dragelj J, Karafoulidi-Retsou C, Katz S, Lenz O, Zebger I, Caserta G, Sacquin-Mora S, Mroginski MAndrea.  2023.  Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator. Frontiers in Microbiology. 13
Nguyen PHoang, Derreumaux P.  2013.  Conformational Ensemble and Polymorphism of the All-Atom Alzheimer's A beta(37-42) Amyloid Peptide Oligomers. J. Phys. Chem. B. 117:5831–5840.
Cazals F, Roth A, Dreyfus T, Mazauric D, Robert CH.  2015.  Conformational ensembles and sampled landscapes: analysis and comparison. J. Comp. Chem.. 36:1213–31.

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