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bpRNA-new

bpRNA-new is a database of single molecule secondary structures annotated using bpRNA.

bpRNA-new is a dataset of RNA families from Rfam 14.2, designed for cross-family validation to assess generalization capability. It focuses on families distinct from those in bpRNA-1m, providing a robust benchmark for evaluating model performance on unseen RNA families.

Disclaimer

This is an UNOFFICIAL release of the bpRNA-new by Kengo Sato, et al.

The team releasing bpRNA-new did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.

Dataset Description

  • bpRNA-1m: A database of single molecule secondary structures annotated using bpRNA.
  • bpRNA-spot: A subset of bpRNA-1m that applies CD-HIT (CD-HIT-EST) to remove sequences with more than 80% sequence similarity from bpRNA-1m.
  • ArchiveII: A database of RNA secondary with the same families as RNAStrAlign, usually used for testing.

License

This dataset is licensed under the GNU Affero General Public License.

For additional terms and clarifications, please refer to our License FAQ.

Text Only
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SPDX-License-Identifier: AGPL-3.0-or-later

Citation

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@article{sato2021rna,
  author    = {Sato, Kengo and Akiyama, Manato and Sakakibara, Yasubumi},
  journal   = {Nature Communications},
  month     = feb,
  number    = 1,
  pages     = {941},
  publisher = {Springer Science and Business Media LLC},
  title     = {{RNA} secondary structure prediction using deep learning with thermodynamic integration},
  volume    = 12,
  year      = 2021
}

Note

The artifacts distributed in this repository are part of the MultiMolecule project. If you use MultiMolecule in your research, you must cite the MultiMolecule project as follows:

BibTeX
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@software{chen_2024_12638419,
  author    = {Chen, Zhiyuan and Zhu, Sophia Y.},
  title     = {MultiMolecule},
  doi       = {10.5281/zenodo.12638419},
  publisher = {Zenodo},
  url       = {https://doi.org/10.5281/zenodo.12638419},
  year      = 2024,
  month     = may,
  day       = 4
}