State-of-the-RNArt visualisations

The code and the predictions from State-of-the-RNArt paper
with three test sets: RNA_PUZZLES, CASP_RNA and RNASOLO.
Code to run the different visualisations of the paper is available in this repository.

We included predictions from AlphaFold 3 as well as 10 other methods.
The predictions are available in the docker_data folder.

Getting started

All the different visualisations can be run in this repository.

Here are some example of the available visualisations:

Heatmap

RNASolo	RNA_Puzzles	CASP_RNA

Box plot

RNASolo	RNA_Puzzles	CASP_RNA

Polar plot

RNASolo	RNA_Puzzles	CASP_RNA

Installation

The installations can be done to do the different visualisations.

To do so, you can use:

pip install -r requirements.txt

Usage

To run the visualisations, one can use:

make viz

or

python -m src.viz_cli

It will run all the visualisations and save them in the docker_data/plots folder.

Metrics computation

You can find the different metrics computation in the docker_data/output folder.

There are metrics computation for the RNA_PUZZLES,CASP_RNA and RNASOLO datasets.

You can recompute the metrics by running:

make run

or

python -m src.benchmark.score_computation

Directory

This repository is organised as follows:

• docker_data: the different predictions from the nine benchmarked tools for RNA_PUZZLES,CASP_RNA and RNASOLO datasets. It also includes the different metrics computation for these datasets (in the docker_data/output folder). The visualisations are saved in the docker_data/plots folder.
• src: the different scripts to run the visualisations and the metrics computation.
• Makefile: a Makefile to run the different scripts.
• requirements.txt: the different requirements to run the scripts.

Citation

If you use this code, please cite the following paper:

Clément Bernard, Guillaume Postic, Sahar Ghannay, Fariza Tahi, 
State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction, 
NAR Genomics and Bioinformatics, Volume 6, Issue 2, June 2024, lqae048, 
https://doi.org/10.1093/nargab/lqae048

Or using the bibtex format:

@article{Bernard2024,
  author = {Clément Bernard and Guillaume Postic and Sahar Ghannay and Fariza Tahi},
  title = {State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction},
  journal = {NAR Genomics and Bioinformatics},
  volume = {6},
  number = {2},
  pages = {lqae048},
  year = {2024},
  month = {June},
  doi = {10.1093/nargab/lqae048},
  url = {https://doi.org/10.1093/nargab/lqae048}
}