@article {2017|2032,
	title = {Conformational Ensembles of the Wild-Type and S8C Aβ1-42 Dimers.},
	journal = {J Phys Chem B},
	volume = {121},
	year = {2017},
	month = {2017 Mar 23},
	pages = {2434-2442},
	abstract = {<p>We characterized the dimer of the amyloid-β wild-type (WT) peptide, Aβ, of 42 residues and its disulfide-bond-locked double mutant (S8C) by replica exchange molecular dynamics simulations. Aβ dimers are known to be the smallest toxic species in Alzheimer\&$\#$39;s disease, and the S8C mutant has been shown experimentally to form an exclusive homogeneous and neurotoxic dimer. Our 50 μs all-atom simulations reveal similar secondary structures and collision cross-sections but very different intramolecular and intermolecular conformations upon double S8C mutation. Both dimers are very dynamic with hundreds of free-energy minima that differ from the U-shape and S-shape conformations of the peptides in the fibrils. The only common structural feature, shared by both species with a probability of 4\% in WT and 12\% in S8C-S8C, is a three-stranded β-sheet spanning the 17-23, 29-36, and 39-41 residues, which does not exist in the Aβ40 WT dimers.</p>
},
	issn = {1520-5207},
	doi = {10.1021/acs.jpcb.7b00267},
	author = {Man, Viet Hoang and Phuong Hoang Nguyen and Philippe Derreumaux}
}
@article {2016|1656,
	title = {Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation},
	journal = {Isr. J. Chem.},
	volume = {DOI: 10.1002/ijch.201600048.},
	year = {2016},
	author = {M. Chiricotto and Thanh-Thuy Tran and Phuong Hoang Nguyen and S. Melchionna and Fabio Sterpone and Philippe Derreumaux}
}
@article {2015|1635,
	title = {Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp},
	journal = {Chemistry-a European Journal},
	volume = {21},
	number = {36},
	year = {2015},
	pages = {12657{\textendash}12666},
	doi = {10.1002/chem.201500888},
	author = {Berthoumieu, Olivia and Phuong Hoang Nguyen and del Castillo-Frias, Maria P. and Ferre, Sabrina and Tarus, Bogdan and Nasica-Labouze, Jessica and Noel, Sabrina and Saurel, Olivier and Rampon, Claire and Doig, Andrew J. and Philippe Derreumaux and Faller, Peter}
}
@article {2015|1768,
	title = {Communication: Multiple atomistic force fields in a single enhanced sampling simulation.},
	journal = {The Journal of Chemical Physics},
	volume = {143},
	number = {2},
	year = {2015},
	month = {jul},
	pages = {021101{\textendash}021101},
	doi = {10.1063/1.4926535},
	author = {Hoang Viet, Man and Philippe Derreumaux and Phuong Hoang Nguyen}
}
@article {2015|1704,
	title = {Communication: Multiple atomistic force fields in a single enhanced sampling simulation},
	journal = {J. Chem. Phys.},
	volume = {143},
	number = {2},
	year = {2015},
	month = {jul},
	pages = {021101},
	doi = {10.1063/1.4926535},
	author = {Man Hoang Viet and Philippe Derreumaux and Phuong Hoang Nguyen}
}
@article {2013|1887,
	title = {Communication: Simulated tempering with fast on-the-fly weight determination},
	journal = {J. Chem. Phys.},
	volume = {138},
	number = {6},
	year = {2013},
	month = {feb},
	pages = {061102},
	doi = {10.1063/1.4792046},
	author = {Phuong Hoang Nguyen and Okamoto, Yuko and Philippe Derreumaux}
}
@article {2013|1924,
	title = {Conformational Ensemble and Polymorphism of the All-Atom Alzheimer{\textquoteright}s A beta(37-42) Amyloid Peptide Oligomers},
	journal = {J. Phys. Chem. B},
	volume = {117},
	number = {19},
	year = {2013},
	month = {may},
	pages = {5831{\textendash}5840},
	doi = {10.1021/jp401563n},
	author = {Phuong Hoang Nguyen and Philippe Derreumaux}
}
@article {2012|1955,
	title = {Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature},
	journal = {Phys. Chem. Chem. Phys.},
	volume = {14},
	number = {20},
	year = {2012},
	pages = {877{\textendash}886},
	doi = {10.1039/c1cp21779h},
	author = {Phuong Hoang Nguyen and Philippe Derreumaux}
}
@article {2011|1473,
	title = {Coherent vibrational energy transfer along a peptide helix},
	journal = {J. Chem. Phys.},
	volume = {134},
	number = {12},
	year = {2011},
	month = {mar},
	author = {Kobus, Maja and Phuong Hoang Nguyen and Stock, Gerhard}
}
@article {2008|1468,
	title = {Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis},
	journal = {J. Chem. Phys.},
	volume = {128},
	number = {24},
	year = {2008},
	month = {jun},
	author = {Altis, Alexandros and Otten, Moritz and Phuong Hoang Nguyen and Hegger, Rainer and Stock, Gerhard}
}
@article {2007|1542,
	title = {Conformational states and folding pathways of peptides revealed by principal-independent component analyses},
	journal = {Proteins: Struct., Funct., Bioinf.},
	volume = {67},
	number = {3},
	year = {2007},
	month = {may},
	pages = {579{\textendash}592},
	author = {Phuong Hoang Nguyen}
}
@article {2006|1541,
	title = {Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis},
	journal = {Proteins: Struct., Funct., Bioinf.},
	volume = {65},
	number = {4},
	year = {2006},
	month = {dec},
	pages = {898{\textendash}913},
	author = {Phuong Hoang Nguyen}
}
