DOI: 10.5281/zenodo.16752003
title: Data, Results, and Scripts for "Decoding RNA Triple Helices: Identification from Sequence and Secondary Structure"

description: This repository contains datasets, results, and scripts associated with a revision of the following manuscript:

Matarrese, M. A. G., Quadrini, M., Luchetti, N., Di Petta, F., Durante, D., Ballarino, M., Chiodo, L., & Tesei, L. (2025). Decoding RNA Triple Helices: Identification from Sequence and Secondary Structure.

The software tool TripleMatcher, used to process the data and generate the results presented in the manuscript, is available at:

https://github.com/bdslab/triplematcher

Please refer to the documentation of the TripleMatcher tool at:

https://github.com/bdslab/triplematcher/blob/master/README.md

dataset/ Folder

This folder contains the three main datasets used in the paper:



ValidationDataset/: Includes full information about the 8 RNA secondary structures used to define and validate the triple helix pattern described in the paper.

Predicted2DValidationDataset/: Contains predicted RNA secondary structures for the same 8 molecules from ValidationDataset, obtained using 8 different folding tools.

Predicted3DValidationDataset/: Contains predicted RNA 3D structures for the same 8 molecules from ValidationDataset, obtained using 4 different 3D prediction tools.

SearchDataset/: A large dataset of RNA secondary structures with associated 3D PDB entries. It is used to identify novel triple helices via the TripleMatcher tool.


This folder includes a README.md file with further details.

results/ Folder

This folder contains the results obtained from processing the datasets using the TripleMatcher tool:



ValidationDatasetResults/: Contains the outputs of the Matcher and 3DFilter components applied to the ValidationDataset, along with validation and zone aggregation data.

Predicted2DValidationDatasetResults/: Contains the outputs of the Matcher and 3DFilter components applied to the PredictedValidationDataset, as well as evaluation metrics and zone aggregation data.

Predicted3DValidationDatasetResults/: Contains the outputs of the Matcher and 3DFilter components applied to the Predicted3DValidationDataset, as well as evaluation metrics and zone aggregation data.

SearchDatasetResults/: Contains the outputs of the Matcher and 3DFilter components applied to the SearchDataset, with additional data on zone aggregation.


This folder includes a README.md file with detailed descriptions of the contents.

scripts/ Folder

This folder contains all the Python scripts used to post-process the output of the TripleMatcher tool and generate the final results reported in the paper.

This folder includes a README.md file with detailed descriptions of the contents.

scripts_v2/ Folder

This folder contains version v2 of all Python and Bash scripts used to post-process the output of the TripleMatcher tool and to generate the final results reported in the paper.

In this updated version, two types of pipelines have been developed:

1.        Pipelines for the SearchDataset and other general datasets.

2.        Pipelines for datasets derived from the ValidationDataset, including those produced by 2D and 3D structure predictions. This pipeline computes the True Positives, False Positives, and False Negatives with respect to the experimental data.

This folder includes a README.md file with detailed descriptions of the contents.

Funding

This work was supported by the European Union - NextGenerationEU - National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.1, under the PRIN 2022 PNRR call (Min. Decree No. 1409, dated September 14, 2022), project: P2022FFEWN RNA secondary structures and their relationship with function: application to non-coding RNAs (RNA2Fun), CUP: J53D23014960001.