||RNA backbone is biologically important with many roles in reactions and interactions,
but has historically been a challenge in structural determination. It has many atoms
and torsions to place, and often there is less data on it than one might wish. This
problem leads to both random and systematic error, producing noise in an already high-dimensional
and complex distribution to further complicate data-driven analysis. With the advent
of the ribosomal subunit structures published in 2000, large RNA structures at good
resolution, it became possible to apply the Richardson laboratory's quality-filtering,
visualization, and analysis techniques to RNA and develop new tools for RNA as well.
A first set of 42 RNA backbone rotamers was identified, developed, and published in
2003; it has since been thoroughly overhauled in conjunction with the backbone group
of the RNA Ontology Consortium to combine the strengths of different approaches, incorporate
new data, and produce a consensus set of 46 conformers. Meanwhile, extensive work
has taken place on developing validation and remodeling tools to correct and improve
existing structures as well as to assist in initial fitting. The use of base-phosphate
perpendicular distances to identify sugar pucker has proven very useful in both hand-refitting
and the semi-automated process of using RNABC (RNA Backbone Correction), a program
developed in conjunction with Dr. Jack Snoeyink's laboratory. The guanine riboswitch
structure ur0039/1U8D, by Dr. Rob Batey's laboratory, has been collaboratively refit
and rerefined as a successful test case of the utility of these tools and techniques.
Their testing and development will continue, and they are expected to help to improve
RNA structure determination in both ease and quality.