@article {2017|2042,
	title = {What Can Human-Guided Simulations Bring to RNA Folding?},
	journal = {Biophys J},
	volume = {113},
	year = {2017},
	month = {2017 Jul 25},
	pages = {302-312},
	abstract = {<p>Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures. Their structures and full trajectories have been analyzed statistically and compared to standard replica exchange molecular dynamics simulations. Our analyses show that participants gain easily chemical intelligence to fold simple and nontrivial topologies, with little computer time, and this result opens the door for the use of human-guided simulations to RNA folding. Our experiment shows that interactive simulations have better chances of success when the user widely explores the conformational space. Interestingly, providing on-the-fly feedback of the root mean square deviation with respect to the experimental structure did not improve the quality of the proposed models.</p>
},
	keywords = {Access to Information, Computer Simulation, Feedback, Psychological, Humans, Internet, Models, Genetic, Models, Molecular, RNA, RNA Folding, Software, Solvents},
	issn = {1542-0086},
	doi = {10.1016/j.bpj.2017.05.047},
	author = {Mazzanti, Liuba and Doutreligne, S{\'e}bastien and Gageat, Cedric and Philippe Derreumaux and Antoine Taly and Marc Baaden and Pasquali, Samuela}
}
@article {2017|2030,
	title = {Why Is Research on Amyloid-β Failing to Give New Drugs for Alzheimer{\textquoteright}s Disease?},
	journal = {ACS Chem Neurosci},
	volume = {8},
	year = {2017},
	month = {2017 Jul 19},
	pages = {1435-1437},
	abstract = {<p>The two hallmarks of Alzheimer\&$\#$39;s disease (AD) are the presence of neurofibrillary tangles (NFT) made of aggregates of the hyperphosphorylated tau protein and of amyloid plaques composed of amyloid-β (Aβ) peptides, primarily Aβ1-40 and Aβ1-42. Targeting the production, aggregation, and toxicity of Aβ with small molecule drugs or antibodies is an active area of AD research due to the general acceptance of the amyloid cascade hypothesis, but thus far all drugs targeting Aβ have failed. From a review of the recent literature and our own experience based on in vitro, in silico, and in vivo studies, we present some reasons to explain this repetitive failure.</p>
},
	keywords = {Alzheimer Disease, Amyloid beta-Peptides, Animals, Drug Discovery, Humans, Neuroprotective Agents},
	issn = {1948-7193},
	doi = {10.1021/acschemneuro.7b00188},
	author = {Doig, Andrew J and Del Castillo-Frias, Maria P and Berthoumieu, Olivia and Tarus, Bogdan and Nasica-Labouze, Jessica and Sterpone, Fabio and Phuong Hoang Nguyen and Hooper, Nigel M and Faller, Peter and Philippe Derreumaux}
}
@conference {2015|1609,
	title = {What Computational Methods can Teach us about the Alzheimer-Protective Nature of A2V-and A2T-Mutant Amyloid-Beta Oligomers},
	booktitle = {Biophys. J.},
	volume = {108},
	number = {2},
	year = {2015},
	pages = {204A-204A},
	author = {Nasica-Labouze, Jessica and Tarus, Bogdan and Phuong Hoang Nguyen and Philippe Derreumaux}
}
@conference {2014|1783,
	title = {Wide Exploration of OPEP Protein Energy Landscapes using Advanced Monte Carlo Methods},
	booktitle = {Biophys. J.},
	volume = {106},
	number = {2, 1},
	year = {2014},
	note = {58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014},
	month = {jan},
	pages = {256A},
	author = {Cragnolini, Tristan and Sutherland-Cash, Kyle H. and Wales, David and Pasquali, Samuela and Philippe Derreumaux}
}
