Publications

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Journal Article
Man VHoang, He X, Derreumaux P, Ji B, Xie X-Q, Nguyen PHoang, Wang J.  2019.  Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: the case of aβ16–22 dimer. Journal of chemical theory and computation. 15:1440–1452.
Nguyen PHoang, Li MSuan, Derreumaux P.  2011.  Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer. Phys. Chem. Chem. Phys.. 13:9778–9788.
Viet MHoang, Nguyen PHoang, Ngo STung, Li MSuan, Derreumaux P.  2013.  Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of A beta(40) and A beta(42). Acs Chem. Neurosci.. 4:1446–1457.
Viet MHoang, Nguyen PHoang, Derreumaux P, Li MSuan.  2014.  Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of A beta 40 and A beta 42. Acs Chem. Neurosci.. 5:646–657.
Nguyen PHoang, Sterpone F, Pouplana R, Derreumaux P, Campanera JM.  2016.  Dimerization Mechanism of Alzheimer A beta(40) Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation. J. Phys. Chem. B. 120:12111–12126.
Altis A, Nguyen PHoang, Hegger R, Stock G.  2007.  Dihedral angle principal component analysis of molecular dynamics simulations. J. Chem. Phys.. 126
Altis A, Otten M, Nguyen PHoang, Hegger R, Stock G.  2008.  Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis. J. Chem. Phys.. 128
Nguyen PHoang.  2007.  Conformational states and folding pathways of peptides revealed by principal-independent component analyses. Proteins: Struct., Funct., Bioinf.. 67:579–592.
Man VHoang, Nguyen PHoang, Derreumaux P.  2017.  Conformational Ensembles of the Wild-Type and S8C Aβ1-42 Dimers.. J Phys Chem B. 121(11):2434-2442.
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.
Nguyen PHoang, Derreumaux P.  2012.  Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature. Phys. Chem. Chem. Phys.. 14:877–886.
Nguyen PHoang.  2006.  Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis. Proteins: Struct., Funct., Bioinf.. 65:898–913.
Nguyen PHoang, Okamoto Y, Derreumaux P.  2013.  Communication: Simulated tempering with fast on-the-fly weight determination. J. Chem. Phys.. 138:061102.
Viet MHoang, Derreumaux P, Nguyen PHoang.  2015.  Communication: Multiple atomistic force fields in a single enhanced sampling simulation. J. Chem. Phys.. 143:021101.
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.
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.
Kobus M, Nguyen PHoang, Stock G.  2011.  Coherent vibrational energy transfer along a peptide helix. J. Chem. Phys.. 134
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.
Domin D, Man VHoang, Van-Oanh N-T, Wang J, Kawasaki T, Derreumaux P, Nguyen PHoang.  2018.  Breaking down cellulose fibrils with a mid-infrared laser. Cellulose. 25:5553–5568.
Nguyen HLinh, Thu TThi Minh, Truong PMinh, Lan PDang, Man VHoang, Nguyen PHoang, Tu LAnh, Chen Y-C, Li MSuan.  2016.  Aβ41 Aggregates More Like Aβ40 than Like Aβ42: In Silico and in Vitro Study. The Journal of Physical Chemistry B. 120:7371–7379.
Nguyen PHoang, Del Castillo-Frias MP, Berthoumieux O, Faller P, Doig AJ, Derreumaux P.  2018.  Amyloid-β/drug interactions from computer simulations and cell-based assays. Journal of Alzheimer's Disease. 64:S659–S672.
Lu Y, Shi X-F, Nguyen PHoang, Sterpone F, Jr FRSalsbury, Derreumaux P.  2019.  Amyloid-β (29–42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids. The Journal of Physical Chemistry B. 123:2687–2696.
Nguyen PHoang, Li MSuan, Derreumaux P.  2014.  Amyloid oligomer structure characterization from simulations: A general method. J. Chem. Phys.. 140:094105.
Nasica-Labouze J, Nguyen PHoang, Sterpone F, Berthoumieu O, Buchete N-V, Cote S, De Simone A, Doig AJ, Faller P, Garcia A et al..  2015.  Amyloid beta Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev.. 115:3518–3563.
Nguyen PHoang, Sterpone F, Derreumaux P.  2020.  Aggregation of disease-related peptides.. Prog Mol Biol Transl Sci. 170:435-460.

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