@article {2020|2116,
	title = {Stability of Aβ11-40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation},
	journal = {The Journal of Physical Chemistry B},
	year = {2020},
	author = {Ngo, Son Tung and Phuong Hoang Nguyen and Philippe Derreumaux}
}
@article {2017|2040,
	title = {Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42).},
	journal = {J Chem Phys},
	volume = {146},
	year = {2017},
	month = {2017 Apr 14},
	pages = {145101},
	abstract = {<p>The formation of senile plaques in central neural system resulting from the aggregation of the amyloid β (Aβ) of 40 and 42 residues is one of the two hallmarks of Alzheimer\&$\#$39;s disease. Numerous experiments and computational studies have shown that the aggregation of Aβ peptides in vitro is very complex and depends on many factors such as pH, agitation, temperature, and peptide concentration. The impact of a static electric field (EF) on amyloid peptide aggregation has been much less studied, although EFs may have some applications to treat Parkinson\&$\#$39;s disease symptoms. Here, we study the influence of an EF strength of 20 mV/nm, present in the human brains, on the conformation of the Aβdimer. Our 7 μs non-equilibrium atomistic simulations in aqueous solution show that this field-strength promotes substantially the formation of β-hairpins, believed to be a very important intermediate state during aggregation. This work also suggests that structural biology experiments conducted under appropriate EF strengths may help reduce the conformational heterogeneity of Aβ/Aβdimers and provide significant insights into their structures that may be disease-causing.</p>
},
	issn = {1089-7690},
	doi = {10.1063/1.4979866},
	author = {Lu, Yan and Shi, Xiao-Feng and Salsbury, Freddie R and Philippe Derreumaux}
}
@article {2015|1714,
	title = {Structures of the Alzheimer{\textquoteright}s Wild-Type A beta 1-40 Dimer from Atomistic Simulations},
	journal = {J. Phys. Chem. B},
	volume = {119},
	number = {33},
	year = {2015},
	pages = {10478{\textendash}10487},
	doi = {10.1021/acs.jpcb.5b05593},
	author = {Tarus, Bogdan and Thanh-Thuy Tran and Nasica-Labouze, Jessica and Fabio Sterpone and Phuong Hoang Nguyen and Philippe Derreumaux}
}
@article {2012|1886,
	title = {Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: Insights from coarse-grained simulations},
	journal = {J. Chem. Phys.},
	volume = {137},
	number = {2},
	year = {2012},
	month = {jul},
	pages = {025101},
	doi = {10.1063/1.4732761},
	author = {Lu, Yan and Wei, Guanghong and Philippe Derreumaux}
}
@article {2012|1921,
	title = {Structures of A beta 17-42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure},
	journal = {J. Phys. Chem. B},
	volume = {116},
	number = {29, SI},
	year = {2012},
	month = {jul},
	pages = {8412{\textendash}8422},
	doi = {10.1021/jp2118778},
	author = {Y Chebaro and Jiang, Ping and Zang, Tong and Mu, Yuguang and Phuong Hoang Nguyen and Mousseau, Normand and Philippe Derreumaux}
}
@article {2011|1782,
	title = {Simulation of the Oligomerization Pathway for Different Alloforms of the Amyloid Beta Protein Related to Alzheimer{\textquoteright}s Disease},
	journal = {Biophys. J.},
	volume = {100},
	number = {3, 1},
	year = {2011},
	note = {55th Annual Meeting of the Biophysical-Society, Baltimore, MD, MAR 05-09, 2011},
	month = {feb},
	pages = {401},
	author = {Cote, Sebastien and Laghaei, Rozita and Philippe Derreumaux and Mousseau, Normand}
}
@article {2009|2009,
	title = {Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations},
	journal = {J. Chem. Phys.},
	volume = {130},
	number = {12},
	year = {2009},
	month = {mar},
	pages = {125101},
	keywords = {Amino Acid Sequence, Amyloid, Humans, Models, Molecular, Molecular Sequence Data, Peptide Fragments, Protein Multimerization, Protein Structure, Quaternary, Solubility, Solvents},
	doi = {10.1063/1.3097982},
	author = {Mo, Yuxiang and Lu, Yan and Wei, Guanghong and Philippe Derreumaux}
}
@article {2009|1916,
	title = {Structures and Thermodynamics of Alzheimer{\textquoteright}s Amyloid-beta A beta(16-35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length A beta Fibrillation},
	journal = {J. Phys. Chem. B},
	volume = {113},
	number = {21},
	year = {2009},
	month = {may},
	pages = {7668{\textendash}7675},
	doi = {10.1021/jp900425e},
	author = {Y Chebaro and Mousseau, Normand and Philippe Derreumaux}
}
@article {2008|1812,
	title = {Self-assembly of amyloid-forming peptides by molecular dynamics simulations},
	journal = {Front. Biosci.},
	volume = {13},
	year = {2008},
	month = {may},
	pages = {5681{\textendash}5692},
	author = {Wei, Guanghong and Song, Wei and Philippe Derreumaux and Mousseau, Normand}
}
@article {2008|1915,
	title = {Self-assembly of the beta 2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals beta-barrel species},
	journal = {J. Phys. Chem. B},
	volume = {112},
	number = {14},
	year = {2008},
	month = {apr},
	pages = {4410{\textendash}4418},
	doi = {10.1021/jp710592v},
	author = {Song, Wei and Wei, Guanghong and Mousseau, Normand and Philippe Derreumaux}
}
@conference {2008|1543,
	title = {Simulating the early steps of amyloid fibril formation and disassembly},
	booktitle = {Publication Series of the John von Neumann Institute for Computing NIC Series},
	volume = {40},
	year = {2008},
	pages = {7{\textendash}12},
	author = {Philippe Derreumaux}
}
@article {2007|1881,
	title = {Sampling small-scale and large-scale conformational changes in proteins and molecular complexes},
	journal = {J. Chem. Phys.},
	volume = {126},
	number = {10},
	year = {2007},
	month = {mar},
	pages = {105101},
	doi = {10.1063/1.2710270},
	author = {Yun, Mi-Ran and Mousseau, N. and Philippe Derreumaux}
}
@article {2007|1616,
	title = {Structural and hydration properties of the partially unfolded states of the prion protein},
	journal = {Biophys. J.},
	volume = {93},
	number = {4},
	year = {2007},
	month = {aug},
	pages = {1284{\textendash}1292},
	doi = {10.1529/biophysj.107.108613},
	author = {De Simone, Alfonso and Zagari, Adriana and Philippe Derreumaux}
}
@article {2007|1617,
	title = {Structure and aggregation mechanism of beta 2-microglobulin (83-99) peptides studied by molecular dynamics Simulations},
	journal = {Biophys. J.},
	volume = {93},
	number = {10},
	year = {2007},
	month = {nov},
	pages = {3353{\textendash}3362},
	doi = {10.1529/biophysj.107.105585},
	author = {Liang, Chungwen and Philippe Derreumaux and Wei, Guanghong}
}
@article {2006|1982,
	title = {Structures of soluble amyloid oligomers from computer simulations},
	journal = {Proteins: Struct., Funct., Bioinf.},
	volume = {65},
	number = {1},
	year = {2006},
	month = {oct},
	pages = {180{\textendash}191},
	doi = {10.1002/prot.21100},
	author = {Melquiond, Adrien and Mousseau, Normand and Philippe Derreumaux}
}
@article {2004|1620,
	title = {Sampling the self-assembly pathways of KFFE hexamers},
	journal = {Biophys. J.},
	volume = {87},
	number = {6},
	year = {2004},
	month = {dec},
	pages = {3648{\textendash}3656},
	doi = {10.1529/biophysj.104.047688},
	author = {Wei, G. H. and Mousseau, N. and Philippe Derreumaux}
}
@article {2004|1787,
	title = {Structural characterization of VGVAPG, an elastin-derived peptide},
	journal = {Biopolymers},
	volume = {76},
	number = {3},
	year = {2004},
	pages = {266{\textendash}280},
	doi = {10.1002/bip.20029},
	author = {Floquet, N and Hery-Huynh, S and Dauchez, M and Philippe Derreumaux and Tamburro, AM and Alix, AJP}
}
@article {2003|1876,
	title = {Sampling the complex energy landscape of a simple beta-hairpin},
	journal = {J. Chem. Phys.},
	volume = {119},
	number = {13},
	year = {2003},
	month = {oct},
	pages = {6403{\textendash}6406},
	doi = {10.1063/1.1613642},
	author = {Wei, GH and Philippe Derreumaux and Mousseau, N}
}
@article {2002|1902,
	title = {Structural modelling of the Sm-like protein Hfq from Escherichia coli},
	journal = {J. Mol. Biol.},
	volume = {320},
	number = {4},
	year = {2002},
	month = {jul},
	pages = {705{\textendash}712},
	doi = {10.1016/S0022-2836(02)00548-X},
	author = {Arluison, V and Philippe Derreumaux and Allemand, F and Folichon, M and Hajnsdorf, E and Regnier, P}
}
@article {2001|1903,
	title = {Sampling activated mechanisms in proteins with the activation-relaxation technique},
	journal = {Journal of Molecular Graphics \& Modelling},
	volume = {19},
	number = {1},
	year = {2001},
	pages = {78{\textendash}86},
	doi = {10.1016/S1093-3263(00)00134-0},
	author = {Mousseau, N and Philippe Derreumaux and Barkema, GT and Malek, R}
}
@article {1993|1906,
	title = {THE STRUCTURES AND VIBRATIONAL FREQUENCIES OF A SERIES OF ALKANES USING THE SPASIBA FORCE-FIELD},
	journal = {J. Mol. Struct.},
	volume = {295},
	year = {1993},
	month = {may},
	pages = {203{\textendash}221},
	doi = {10.1016/0022-2860(93)85021-L},
	author = {Philippe Derreumaux and Dauchez, M and VERGOTEN, G}
}
