Welcome to RNAGlib’s Documentation!

RNAglib is a Python package for studying RNA 2.5D structures. Functionality includes automated data loading, analysis, visualization, ML model building and benchmarking.

  • What are RNA 2.5D structures?

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 (graph-level)

  • Protein binding (node-level)

  • Small molecule binding (node-level)

  • Chemical modifications (node-level)

  • 3-D coordinates(node-level)

  • Leontis-westhof base pair geometry classification (edge-level)

We provide a visualization of what the graphs in this database contain. A more detailed description of the data is presented in rnaglib.data. Example graph

Package Structure

Installation

The package can be cloned and the source code used directly. We also deploy it as a pip package and recommend using this install in conda environments.

If one wants to use GPU support, one should install Pytorch and DGL with the appropriate options. Otherwise you can just skip this step and the pip installs of Pytorch and DGL will be used.

Then, one just needs to run :

pip install rnaglib

and can start using the packages functionalities by importing them in one’s python script.

To have an idea on how to use the main functions of RNAGlib, please visit Quickstart

Associated Repositories:

RNAMigos : a research paper published in Nucleic Acid Research that demonstrates the usefulness of 2.5D graphs for machine learning tasks, exemplified onto the drug discovery application.

VeRNAl : a research paper published in Bioinformatics that uses learnt vector representations of RNA subgraphs to mine structural motifs in RNA.

References

  1. Leontis, N. B., & Zirbel, C. L. (2012). Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking. In RNA 3D Structure Analysis and Prediction N. Leontis & E. Westhof (Eds.), (Vol. 27, pp. 281–298). Springer Berlin Heidelberg. doi:10.1007/978-3-642-25740-7\_13

Indices and tables