@article {2017|2041,
	title = {Fast coarse-grained model for RNA titration.},
	journal = {J Chem Phys},
	volume = {146},
	year = {2017},
	month = {2017 Jan 21},
	pages = {035101},
	abstract = {<p>A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-H{\"u}ckel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKshifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.</p>
},
	keywords = {Azotobacter vinelandii, Introns, Models, Chemical, Molecular Dynamics Simulation, Monte Carlo Method, Protein Structure, Secondary, Protons, RNA, RNA, Catalytic, Titrimetry},
	issn = {1089-7690},
	doi = {10.1063/1.4972986},
	author = {Barroso da Silva, Fernando Luis and Philippe Derreumaux and Pasquali, Samuela}
}
@article {2015|1713,
	title = {Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering},
	journal = {J. Phys. Chem. B},
	volume = {119},
	number = {23},
	year = {2015},
	month = {jun},
	pages = {6941{\textendash}6951},
	author = {Zhang, Tong and Phuong Hoang Nguyen and Nasica-Labouze, Jessica and Mu, Yuguang and Philippe Derreumaux}
}
@article {2014|1927,
	title = {Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the A beta 1-28 Monomer},
	journal = {J. Phys. Chem. B},
	volume = {118},
	number = {2},
	year = {2014},
	month = {jan},
	pages = {501{\textendash}510},
	doi = {10.1021/jp4115404},
	author = {Phuong Hoang Nguyen and Tarus, Bogdan and Philippe Derreumaux}
}
@article {2012|1932,
	title = {Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches},
	journal = {Journal of the Royal Society Interface},
	volume = {9},
	number = {66},
	year = {2012},
	month = {jan},
	pages = {20{\textendash}33},
	doi = {10.1098/rsif.2011.0584},
	author = {Pierre Tuffery and Philippe Derreumaux}
}
@article {2010|1901,
	title = {A Fast Method for Large-Scale De Novo Peptide and Miniprotein Structure Prediction},
	journal = {J. Comput. Chem.},
	volume = {31},
	number = {4},
	year = {2010},
	month = {mar},
	pages = {726{\textendash}738},
	doi = {10.1002/jcc.21365},
	author = {Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery}
}
@article {2009|1436,
	title = {A fast method for large-scale De Novo peptide and miniprotein structure prediction.},
	journal = {J. Comput. Chem.},
	year = {2009},
	month = {jun},
	doi = {10.1002/jcc.21365},
	author = {Julien Maupetit and Philippe Derreumaux and Pierre Tuffery}
}
@conference {2008|1544,
	title = {Free energy surface of Abeta(16-22) complexed by N-methylated Abeta16-22 inhibitors},
	booktitle = {Publication Series of the John von Neumann Institute for Computing NIC Series},
	volume = {40},
	year = {2008},
	pages = {177{\textendash}179},
	author = {Y Chebaro and Philippe Derreumaux}
}
@article {2005|1879,
	title = {Following the aggregation of amyloid-forming peptides by computer simulations},
	journal = {J. Chem. Phys.},
	volume = {122},
	number = {17},
	year = {2005},
	month = {may},
	pages = {174904},
	doi = {10.1063/1.1886725},
	author = {Melquiond, A and Boucher, G and Mousseau, N and Philippe Derreumaux}
}
@conference {2005,
	title = {Following the aggregation of amyloid-forming peptides by computer simulations.},
	booktitle = {Abstracts of Papers of the American Chemical Society},
	volume = {229},
	number = {Part 2},
	year = {2005},
	pages = {U735},
	author = {Philippe Derreumaux}
}
@article {1999|1873,
	title = {From polypeptide sequences to structures using Monte Carlo simulations and an optimized potential},
	journal = {J. Chem. Phys.},
	volume = {111},
	number = {5},
	year = {1999},
	month = {aug},
	pages = {2301{\textendash}2310},
	doi = {10.1063/1.479501},
	author = {Philippe Derreumaux}
}
@article {1998|1872,
	title = {Finding the low-energy forms of avian pancreatic polypeptide with the diffusion-process-controlled Monte Carlo method},
	journal = {J. Chem. Phys.},
	volume = {109},
	number = {4},
	year = {1998},
	month = {jul},
	pages = {1567{\textendash}1574},
	doi = {10.1063/1.476708},
	author = {Philippe Derreumaux}
}
@article {1997|1870,
	title = {Folding a 20 amino acid alpha beta peptide with the diffusion process-controlled Monte Carlo method},
	journal = {J. Chem. Phys.},
	volume = {107},
	number = {6},
	year = {1997},
	month = {aug},
	pages = {1941{\textendash}1947},
	doi = {10.1063/1.474546},
	author = {Philippe Derreumaux}
}
@article {1994|1992,
	title = {FORCE-FIELD AND VIBRATIONAL-SPECTRA OF OLIGOSACCHARIDES WITH DIFFERENT GLYCOSIDIC LINKAGES .1. TREHALOSE DIHYDRATE, SOPHOROSE MONOHYDRATE AND LAMINARIBIOSE},
	journal = {Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy},
	volume = {50},
	number = {1},
	year = {1994},
	month = {jan},
	pages = {87{\textendash}104},
	doi = {10.1016/0584-8539(94)80117-7},
	author = {Dauchez, M and Philippe Derreumaux and LAGANT, P and VERGOTEN, G and SEKKAL, M and LEGRAND, P}
}
@article {1994|1993,
	title = {FORCE-FIELD AND VIBRATIONAL-SPECTRA OF OLIGOSACCHARIDES WITH DIFFERENT GLYCOSIDIC LINKAGES .2. MALTOSE MONOHYDRATE, CELLOBIOSE AND GENTIOBIOSE},
	journal = {Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy},
	volume = {50},
	number = {1},
	year = {1994},
	month = {jan},
	pages = {105{\textendash}118},
	doi = {10.1016/0584-8539(94)80118-5},
	author = {Dauchez, M and LAGANT, P and Philippe Derreumaux and VERGOTEN, G and SEKKAL, M and SOMBRET, B}
}
