title: Advances in RNA molecular dynamics: a simulator's guide to RNA force fields.
abstract: Molecular simulations have become an essential tool for biochemical research. When they work properly, they are able to provide invaluable interpretations of experimental results and ultimately provide novel, experimentally testable predictions. Unfortunately, not all simulation models are created equal, and with inaccurate models it becomes unclear what is a bona fide prediction versus a simulation artifact. RNA models are still in their infancy compared to the many robust protein models that are widely in use, and for that reason the number of RNA force field revisions in recent years has been rapidly increasing. As there is no universally accepted 'best' RNA force field at the current time, RNA simulators must decide which one is most suited to their purposes, cognizant of its essential assumptions and their inherent strengths and weaknesses. Hopefully, armed with a better understanding of what goes inside the simulation 'black box,' RNA biochemists can devise novel experiments and provide crucial thermodynamic and structural data that will guide the development and testing of improved RNA models. WIREs RNA 2017, 8:e1396. doi: 10.1002/wrna.1396 For further resources related to this article, please visit the WIREs website.
authors.affiliation: The RNA Institute, University at Albany State University of New York, Albany, NY, USA.
authors.forename: Sweta
authors.initials: S
authors.lastname: Vangaveti
authors.affiliation: The RNA Institute, University at Albany State University of New York, Albany, NY, USA.
authors.forename: Srivathsan V
authors.initials: SV
authors.lastname: Ranganathan
authors.affiliation: The RNA Institute, University at Albany State University of New York, Albany, NY, USA.|Department of Chemistry, University at Albany State University of New York, Albany, NY, USA.
authors.forename: Alan A
authors.identifier: 0000-0001-8246-2935
authors.initials: AA
authors.lastname: Chen
mesh_terms: D000818:Animals; D006801:Humans; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA