@article {2022|2161,
	title = {Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]},
	journal = {Living Journal of Computational Molecular Science},
	volume = {4},
	year = {2022},
	month = {Dec.},
	pages = {1583},
	abstract = {<p>Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation time. This review aims to present the unifying principles of and differences between many of the computational methods currently used for enhanced sampling in molecular simulations of biomolecules, soft matter and molecular crystals. In fact, despite the apparent abundance and divergence of such methods, the principles at their core can be boiled down to a relatively limited number of statistical and physical concepts. To enable comparisons, the various methods are introduced using similar terminology and notation. We then illustrate in which ways many different methods combine features of a relatively small number of the same enhanced sampling concepts. This review is intended for scientists with an understanding of the basics of molecular dynamics simulations and statistical physics who want a deeper understanding of the ideas that underlie various enhanced sampling methods and the relationships between them. This living review is intended to be updated to continue to reflect the wealth of sampling methods as they continue to emerge in the literature.</p>
},
	doi = {10.33011/livecoms.4.1.1583},
	url = {https://livecomsjournal.org/index.php/livecoms/article/view/v4i1e1583},
	author = {J{\'e}r{\^o}me H{\'e}nin and Leli{\`e}vre, Tony and Shirts, Michael R. and Valsson, Omar and Delemotte, Lucie}
}
@article {2016|1746,
	title = {Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors.},
	journal = {Plos One},
	volume = {11},
	year = {2016},
	pages = {e0151934},
	abstract = {<p>Pentameric ligand-gated ion channels (pLGICs) are ubiquitous neurotransmitter receptors in Bilateria, with a small number of known prokaryotic homologues. Here we describe a new inventory and phylogenetic analysis of pLGIC genes across all kingdoms of life. Our main finding is a set of pLGIC genes in unicellular eukaryotes, some of which are metazoan-like Cys-loop receptors, and others devoid of Cys-loop cysteines, like their prokaryotic relatives. A number of such \&quot;Cys-less\&quot; receptors also appears in invertebrate metazoans. Together, those findings draw a new distribution of pLGICs in eukaryotes. A broader distribution of prokaryotic channels also emerges, including a major new archaeal taxon, Thaumarchaeota. More generally, pLGICs now appear nearly ubiquitous in major taxonomic groups except multicellular plants and fungi. However, pLGICs are sparsely present in unicellular taxa, suggesting a high rate of gene loss and a non-essential character, contrasting with their essential role as synaptic receptors of the bilaterian nervous system. Multiple alignments of these highly divergent sequences reveal a small number of conserved residues clustered at the interface between the extracellular and transmembrane domains. Only the \&quot;Cys-loop\&quot; proline is absolutely conserved, suggesting the more fitting name \&quot;Pro loop\&quot; for that motif, and \&quot;Pro-loop receptors\&quot; for the superfamily. The infered molecular phylogeny shows a Cys-loop and a Cys-less clade in eukaryotes, both containing metazoans and unicellular members. This suggests new hypotheses on the evolutionary history of the superfamily, such as a possible origin of the Cys-loop cysteines in an ancient unicellular eukaryote. Deeper phylogenetic relationships remain uncertain, particularly around the split between bacteria, archaea, and eukaryotes.</p>},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0151934},
	author = {Jaiteh, Mariama and Antoine Taly and J{\'e}r{\^o}me H{\'e}nin}
}
@article {2010|1851,
	title = {Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables},
	journal = {J. Chem. Theory Comput.},
	volume = {6},
	number = {1},
	year = {2010},
	pages = {35{\textendash}47},
	author = {J{\'e}r{\^o}me H{\'e}nin and Giacomo Fiorin and Christophe Chipot and Michael L Klein}
}
@article {2008|1970,
	title = {Embedded cholesterol in the nicotinic acetylcholine receptor},
	journal = {Proc. Natl. Acad. Sci. U.s.a.},
	volume = {105},
	number = {38},
	year = {2008},
	pages = {14418{\textendash}14423},
	publisher = {Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. grace@cmm.upenn.edu},
	abstract = {The nicotinic acetylcholine receptor (nAChR) is a cation-selective channel central to both neuronal and muscular processes and is considered the prototype for ligand-gated ion channels, motivating a structural determination effort that spanned several decades [Unwin N (2005) Refined structure of the nicotinic acetylcholine receptor at 4 A resolution. J Mol Biol 346:967-989]. Purified nAChR must be reconstituted in a mixture containing cholesterol to function. Proposed modes of interaction between cholesterol and the protein range from specific binding to indirect membrane-mediated mechanisms. However, the underlying cause of nAChR sensitivity to cholesterol remains controversial, in part because the vast majority of functional studies were conducted before a medium resolution structure was reported. We show that the nAChR contains internal sites capable of containing cholesterol, whose occupation stabilizes the protein structure. We detect sites at the protein-lipid interface as conventionally predicted from functional data, as well as deeply buried sites that are not usually considered. Molecular dynamics simulations reveal that occupation of both superficial and deeply buried sites most effectively preserves the experimental structure; the structure collapses in the absence of bound cholesterol. In particular, we find that bound cholesterol directly supports contacts between the agonist-binding domain and the pore that are thought to be essential for activation of the receptor. These results likely apply to those other ion channels within the Cys-loop superfamily that depend on cholesterol, such as the GABA receptor.},
	doi = {10.1073/pnas.0803029105},
	author = {Grace Brannigan and J{\'e}r{\^o}me H{\'e}nin and Richard Law and Roderic G Eckenhoff and Michael L Klein}
}
@article {2005|1847,
	title = {Exploring the free energy landscape of a short peptide using an average force},
	journal = {J. Chem. Phys.},
	volume = {123},
	year = {2005},
	pages = {244906},
	author = {Christophe Chipot and J{\'e}r{\^o}me H{\'e}nin}
}
