Data, Results, and Scripts for “Decoding RNA Triple Helices: Identification from Sequence and Secondary Structure”

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:

• ValidationD
  

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