Improved prediction of RNA tertiary structure with insights into native state dynamics

Statistical potentials. (A) Base doublet quality is analyzed through five variables x, y, z, ϕ₂, and θ₂ that define the relative position of any two bases. (B) Voronoi polyhedra are constructed around all atoms so that volumes, surfaces, and neighbors can be determined quantitatively. Atoms that share faces with the bounding box are considered unpacked. A U-A base pair is shown as an example. (C) Hydrogen bond probability is scored based on parameters θ₁, θ₂, and ρ based on the model proposed by Lemieux and Major (2002).