@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 {2015|1755,
	title = {How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory.},
	journal = {Proc. Natl. Acad. Sci. Usa},
	volume = {112},
	year = {2015},
	pages = {9270{\textendash}5},
	abstract = {<p>It is currently the consensus belief that protective osmolytes such as trimethylamine N-oxide (TMAO) favor protein folding by being excluded from the vicinity of a protein, whereas denaturing osmolytes such as urea lead to protein unfolding by strongly binding to the surface. Despite there being consensus on how TMAO and urea affect proteins as a whole, very little is known as to their effects on the individual mechanisms responsible for protein structure formation, especially hydrophobic association. In the present study, we use single-molecule atomic force microscopy and molecular dynamics simulations to investigate the effects of TMAO and urea on the unfolding of the hydrophobic homopolymer polystyrene. Incorporated with interfacial energy measurements, our results show that TMAO and urea act on polystyrene as a protectant and a denaturant, respectively, while complying with Tanford-Wyman preferential binding theory. We provide a molecular explanation suggesting that TMAO molecules have a greater thermodynamic binding affinity with the collapsed conformation of polystyrene than with the extended conformation, while the reverse is true for urea molecules. Results presented here from both experiment and simulation are in line with earlier predictions on a model Lennard-Jones polymer while also demonstrating the distinction in the mechanism of osmolyte action between protein and hydrophobic polymer. This marks, to our knowledge, the first experimental observation of TMAO-induced hydrophobic collapse in a ternary aqueous system.</p>},
	keywords = {Atomic Force, Computer Simulation, Hydrophobic and Hydrophilic Interactions, Mechanical, Methylamines, Methylamines: chemistry, Microscopy, Molecular Dynamics Simulation, Normal Distribution, Polymers, Polymers: chemistry, Polystyrenes, Polystyrenes: chemistry, Protein Binding, Protein Conformation, Protein Folding, Proteins, Proteins: chemistry, Software, Solvents, Solvents: chemistry, Stress, Thermodynamics, Urea, Urea: chemistry, Water, Water: chemistry},
	isbn = {1215421109},
	issn = {1091-6490},
	doi = {10.1073/pnas.1511780112},
	url = {http://www.pnas.org/content/112/30/9270},
	author = {Mondal, Jagannath and Halverson, Duncan and Li, Isaac T S and Guillaume Stirnemann and Walker, Gilbert C and Berne, Bruce J}
}
@article {2009|1830,
	title = {Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.},
	journal = {J. Phys. Chem. B},
	volume = {113},
	number = {1},
	year = {2009},
	month = {jan},
	pages = {267{\textendash}274},
	keywords = {Amino Acid Sequence, Computer Simulation, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Peptides, Protein Folding, Protein Structure, Proteins, Secondary, Solvents, Temperature, Thermodynamics},
	doi = {10.1021/jp805309e},
	author = {Y Chebaro and Xiao Dong and Rozita Laghaei and Philippe Derreumaux and Normand Mousseau}
}
@article {2009|2009,
	title = {Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations},
	journal = {J. Chem. Phys.},
	volume = {130},
	number = {12},
	year = {2009},
	month = {mar},
	pages = {125101},
	keywords = {Amino Acid Sequence, Amyloid, Humans, Models, Molecular, Molecular Sequence Data, Peptide Fragments, Protein Multimerization, Protein Structure, Quaternary, Solubility, Solvents},
	doi = {10.1063/1.3097982},
	author = {Mo, Yuxiang and Lu, Yan and Wei, Guanghong and Philippe Derreumaux}
}
