@article {2019|2110,
	title = {Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: the case of aβ16{\textendash}22 dimer},
	journal = {Journal of chemical theory and computation},
	volume = {15},
	year = {2019},
	pages = {1440{\textendash}1452},
	author = {Man, Viet Hoang and He, Xibing and Philippe Derreumaux and Ji, Beihong and Xie, Xiang-Qun and Phuong Hoang Nguyen and Wang, Junmei}
}
@article {2016|1765,
	title = {Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin},
	journal = {Soft Matter},
	volume = {12},
	number = {25},
	year = {2016},
	pages = {5600{\textendash}5612},
	abstract = {Spider silk is a fascinating material combining mechanical properties such as maximum strength and high toughness comparable or better than man-made materials, with biocompatible degradability characteristics. Experimental measurements have shown that pH triggers the dimer formation of the N-terminal domain (NTD) of the major ampullate spidroin 1 (MaSp 1). A coarse-grained model accounting for electrostatics, van der Waals and pH-dependent charge-fluctuation interactions, by means of Monte Carlo simulations, gave us a more comprehensive view of the NTD dimerization process. A detailed analysis of the electrostatic properties and free energy derivatives for the NTD homoassociation was carried out at different pH values and salt concentrations for the protein wild type and for several mutants. We observed an enhancement of dipole-dipole interactions at pH 6 due to the ionization of key amino acids, a process identified as the main driving force for dimerization. Analytical estimates based on the DVLO theory framework corroborate our findings. Molecular dynamics simulations using the OPEP coarse-grained force field for proteins show that the mutant E17Q is subject to larger structural fluctuations when compared to the wild type. Estimates of the association rate constants for this mutant were evaluated by the Debye-Smoluchowski theory and are in agreement with the experimental data when thermally relaxed structures are used instead of the crystallographic data. Our results can contribute to the design of new mutants with specific association properties.},
	issn = {1744-683X},
	doi = {10.1039/c6sm00860g},
	author = {Barroso da Silva, Fernando Luis and Pasquali, Samuela and Philippe Derreumaux and Dias, Luis Gustavo}
}
@article {2016|1630,
	title = {Evaluation of the coarse-grained OPEP force field for protein-protein docking},
	journal = {Bmc Biophysics},
	volume = {9},
	year = {2016},
	month = {apr},
	abstract = {Background: Knowing the binding site of protein-protein complexes helps understand their function and shows possible regulation sites. The ultimate goal of protein-protein docking is the prediction of the three-dimensional structure of a protein-protein complex. Docking itself only produces plausible candidate structures, which must be ranked using scoring functions to identify the structures that are most likely to occur in nature. Methods: In this work, we rescore rigid body protein-protein predictions using the optimized potential for efficient structure prediction (OPEP), which is a coarse-grained force field. Using a force field based on continuous functions rather than a grid-based scoring function allows the introduction of protein flexibility during the docking procedure. First, we produce protein-protein predictions using ZDOCK, and after energy minimization via OPEP we rank them using an OPEP-based soft rescoring function. We also train the rescoring function for different complex classes and demonstrate its improved performance for an independent dataset. Results: The trained rescoring function produces a better ranking than ZDOCK for more than 50 \% of targets, rising to over 70 \% when considering only enzyme/inhibitor complexes. Conclusions: This study demonstrates for the first time that energy functions derived from the coarse-grained OPEP force field can be employed to rescore predictions for protein-protein complexes.},
	issn = {2046-1682},
	doi = {10.1186/s13628-016-0029-y},
	author = {Kynast, Philipp and Philippe Derreumaux and Strodel, Birgit}
}
@article {2015|1780,
	title = {{E}pock: rapid analysis of protein pocket dynamics},
	journal = {Bioinformatics},
	volume = {31},
	number = {9},
	year = {2015},
	month = {may},
	pages = {1478{\textendash}1480},
	doi = {10.1093/bioinformatics/btu822},
	author = {Laurent, Benoist and Matthieu Chavent and Cragnolini, Tristan and Dahl, Anna Caroline E. and Pasquali, Samuela and Philippe Derreumaux and Sansom, Mark S. P. and Marc Baaden}
}
@article {2014|1379,
	title = {Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of A beta 40 and A beta 42},
	journal = {Acs Chem. Neurosci.},
	volume = {5},
	number = {8},
	year = {2014},
	month = {aug},
	pages = {646{\textendash}657},
	author = {Man Hoang Viet and Phuong Hoang Nguyen and Philippe Derreumaux and Li, Mai Suan}
}
@article {2013,
	title = {Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of A beta(40) and A beta(42)},
	journal = {Acs Chem. Neurosci.},
	volume = {4},
	number = {11},
	year = {2013},
	month = {nov},
	pages = {1446{\textendash}1457},
	author = {Man Hoang Viet and Phuong Hoang Nguyen and Son Tung Ngo and Li, Mai Suan and Philippe Derreumaux}
}
@article {2011|1953,
	title = {Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer},
	journal = {Phys. Chem. Chem. Phys.},
	volume = {13},
	number = {20},
	year = {2011},
	pages = {9778{\textendash}9788},
	doi = {10.1039/c1cp20323a},
	author = {Phuong Hoang Nguyen and Li, Mai Suan and Philippe Derreumaux}
}
@article {2011|1919,
	title = {Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-beta Fragment 29-42 by Replica Exchange Molecular Dynamics Simulations},
	journal = {J. Phys. Chem. B},
	volume = {115},
	number = {5},
	year = {2011},
	month = {feb},
	pages = {1282{\textendash}1288},
	doi = {10.1021/jp110269a},
	author = {Lu, Yan and Wei, Guanghong and Philippe Derreumaux}
}
@article {2010|1918,
	title = {Effects of the RGTFEGKF Inhibitor on the Structures of the Transmembrane Fragment 70-86 of Glycophorin A: An All-Atom Molecular Dynamics Study},
	journal = {J. Phys. Chem. B},
	volume = {114},
	number = {2},
	year = {2010},
	month = {jan},
	pages = {1004{\textendash}1009},
	doi = {10.1021/jp908889q},
	author = {Li, Huiyu and Luo, Yin and Philippe Derreumaux and Wei, Guanghong}
}
@article {2009|2018,
	title = {Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study},
	journal = {J. Phys. Chem. B},
	volume = {113},
	number = {27},
	year = {2009},
	month = {jul},
	pages = {9340{\textendash}9347},
	keywords = {Binding Sites, Computer Simulation, Energy Transfer, Guanine, Ligands, Models, Molecular, Nucleic Acid Conformation, RNA, Temperature},
	doi = {10.1021/jp902013s},
	author = {Phuong Hoang Nguyen and Philippe Derreumaux and Stock, Gerhard}
}
@conference {2009,
	title = {Exploring amyloid aggregates with the OPEP coarse-grained force field},
	booktitle = {Abstracts of Papers of the American Chemical Society},
	volume = {238},
	year = {2009},
	author = {Philippe Derreumaux}
}
@article {2008|1883,
	title = {Energy landscapes of the monomer and dimer of the Alzheimer{\textquoteright}s peptide A beta(1-28)},
	journal = {J. Chem. Phys.},
	volume = {128},
	number = {12},
	year = {2008},
	month = {mar},
	pages = {125108},
	doi = {10.1063/1.2890033},
	author = {Dong, Xiao and Chen, Wei and Mousseau, Normand and Philippe Derreumaux}
}
@article {2008|1811,
	title = {Exploring energy landscapes of protein folding and aggregation},
	journal = {Front. Biosci.},
	volume = {13},
	year = {2008},
	month = {may},
	pages = {4495{\textendash}4516},
	doi = {10.2741/3019},
	author = {Mousseau, Normand and Philippe Derreumaux}
}
@article {2005|1378,
	title = {Exploring the early steps of amyloid peptide aggregation by computers},
	journal = {Acc. Chem. Res.},
	volume = {38},
	number = {11},
	year = {2005},
	pages = {885{\textendash}891},
	author = {Mousseau, N and Philippe Derreumaux}
}
@article {2004|1939,
	title = {Early steps of amyloid-petide oligomerisation explored by simulations},
	journal = {Neurobiol. Aging},
	volume = {25},
	number = {Suppl. 2},
	year = {2004},
	month = {jul},
	pages = {S143},
	doi = {10.1016/S0197-4580(04)80481-0},
	author = {Philippe Derreumaux and Wei, GH and Santini, S and Mousseau, NN}
}
@article {2004|1928,
	title = {Exploring the early steps of aggregation of amyloid-forming peptide KFFE},
	journal = {Journal of Physics-condensed Matter},
	volume = {16},
	number = {44, Sp. Iss. SI},
	year = {2004},
	month = {nov},
	pages = {S5047-S5054},
	doi = {10.1088/0953-8984/16/44/002},
	author = {Wei, GH and Mousseau, N and Philippe Derreumaux}
}
@article {2003|1428,
	title = {Exploring the folding pathways of proteins through energy landscape sampling: Application to Alzheimer{\textquoteright}s beta-amyloid peptide},
	journal = {Internet Electron. J. Mol. Des.},
	volume = {2},
	year = {2003},
	pages = {564{\textendash}577},
	author = {S. Santini and G. Wei and N. Mousseau and Philippe Derreumaux}
}
@article {2002|1874,
	title = {Exploring the energy landscape of proteins: A characterization of the activation-relaxation technique},
	journal = {J. Chem. Phys.},
	volume = {117},
	number = {24},
	year = {2002},
	month = {dec},
	pages = {11379{\textendash}11387},
	doi = {10.1063/1.1522373},
	author = {Wei, GH and Mousseau, N and Philippe Derreumaux}
}
@article {2001|1623,
	title = {Evidence that the 127-164 region of prion proteins has two equi-energetic conformations with beta or alpha features},
	journal = {Biophys. J.},
	volume = {81},
	number = {3},
	year = {2001},
	month = {sep},
	pages = {1657{\textendash}1665},
	author = {Philippe Derreumaux}
}
@article {1991|1987,
	title = {EFFECT OF UREY-BRADLEY-SHIMANOUCHI FORCE-FIELD ON THE HARMONIC DYNAMICS OF PROTEINS},
	journal = {Proteins-structure Function and Genetics},
	volume = {11},
	number = {2},
	year = {1991},
	pages = {120{\textendash}132},
	doi = {10.1002/prot.340110205},
	author = {Philippe Derreumaux and VERGOTEN, G}
}
