R K B

Ribonucleic acids are characteristically single-stranded polymers composed of covalently linked nucleotide residues that can fold back on themselves to form anti-parallel double helical secondary structures.

The double-helical structures formed tend to be no longer than 20 base pairs and are usually terminated by unpaired stretches of covalently linked nucleotide residues. The nucleotide base pairs that form the rungs of the helical structures are composed of at least two nucleotide residues that generally form the canonical set of base pairs (AU, UA, CG and GC) and the wobble base pairs (UG and GU).

Canonical base pairs, as described by Leontis and Westhof (2001), occur as a result of the hydrogen bonding between the edges of the bases. Since edges are composed of multiple atoms and hydrogen bonds occur between pairs of atoms, Lemieux and Major (2002) developed a system of atomic level granularity that refers to sub-edges or so-called faces.

The RKB's representation of Nucleotide Base Pairs enables users to use either nomenclature scheme. Where knowledge of the external connectivity of participating nucleotide residues can be specified at the nucleobase level (in the case of the LW scheme) or with more granular description (LW+ scheme) where sub-edge interactions can be specified.

Base stacking involves London dispersion inter-molecular interactions between two nucleotide residues that entail a spatial arrangement where one base is stacked on top of another. Base stacking is defined on the relative orientation of their base normals.

The RKB's representation of base stacks requires for base stacks to bear a base stack base normal orientation quality and a base stack sequence adjacency quality.