What is an RNA 2.5D structure?ΒΆ
RNA 2.5D structures are discrete graph-based representations of atomic coordinates derived from techniques such as X-ray crystallography and NMR. This type of representation encodes all possible base pairing interactions which are known to be crucial for understanding RNA function.
Why use RNA 2.5D data?
The benefit is twofold. When dealing with RNA 3D data, a representation centered on base pairing is a very natural prior which has been shown to carry important signals for complex interactions, and can be directly interpreted. Second, adopting graph representations lets us take advantage of many powerful algorithmic tools such as graph neural networks and graph kernels.
What type of functional data is included?
The graphs are annotated with graph, node, and edge-level attributes. These include, but are not limited to:
Secondary structure
Protein binding
Small molecule binding
Chemical modifications
3-D coordinates
Leontis-westhof base pair geometry classification
We provide a visualization of what the graphs in this database contain. A more detailed description of the data is presented in rnaglib.data.
