Non-Redundant List

Motivation: The continual improvement of methods for RNA 3D structure modeling and prediction requires accurate and statistically meaningful data concerning RNA structure, both for extraction of knowledge and for benchmarking of structure predictions. The source of sufficiently accurate structural data for these purposes is atomic-resolution x-ray structures of RNA nucleotides, oligonucleotides, and biologically functional RNA molecules. All of our basic knowledge of bond lengths, angles, and stereochemistry in RNA nucleotides, as well as their interaction preferences, including all types of base-pairing, base-stacking and base-backbone interactions, is ultimately extracted from x-ray structures. One key requirement for reference databases intended for knowledge extraction is the non-redundancy of the structures that are included in the analysis, to avoid bias in the deduced frequency parameters. For these reasons we have developed this Non-Redundant (or reduced redundancy) data set of RNA-containing, atomic-resolution 3D structures.

Database specifics: The  database is automatically updated on a weekly and ongoing basis. We provide lists at different resolution thresholds for use in knowledge-driven RNA applications. The file collections are available for download at http://rna.bgsu.edu/rna3dhub/nrlist/. The primary lists that we provide only include x-ray structures, organized by resolution thresholds, but for completeness, we also provide separate lists that include structures solved by NMR or cryo-EM.

References

Zirbel and Leontis (2012) “Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking .” Ch 13 in Leontis and Westhof RNA 3D Structure Analysis and Prediction.

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