metadata

language: rna
tags:
  - Biology
  - RNA
license:
  - agpl-3.0
size_categories:
  - 1K<n<10K
task_categories:
  - text-generation
  - fill-mask
task_ids:
  - language-modeling
  - masked-language-modeling
pretty_name: EternaBench-CM
library_name: multimolecule

EternaBench-CM

EternaBench is a database comprising the diverse high-throughput structural data gathered through the crowdsourced RNA design project Eterna, to evaluate the performance of a wide set of structure algorithms.

Disclaimer

This is an UNOFFICIAL release of the EternaBench by Hannah K. Wayment-Steele, et al.

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

Dataset Description

Homepage: https://multimolecule.danling.org/datasets/eternabench
Point of Contact: Rhiju Das

Example Entry

ID	design_name	sequence	structure	reactivity	errors	signal_to_noise
769337-1	d+m plots weaker again	GGAAAAAAAAAAA...	................	[0.642,1.4853,0.1629, ...]	[0.3181,0.4221,0.1823, ...]	3.227

Column Description

The EternaBench dataset consists of the following columns, providing crucial insights for understanding RNA stability for vaccine design:

ID: A unique identifier for each RNA sequence entry.
design_name: The name given to each RNA design by contributors, used for easy reference.
sequence: The nucleotide sequence of the RNA, using standard bases.
structure: The predicted secondary structure of the RNA, represented using dot-bracket notation. The structure helps determine the likely secondary interactions within each RNA molecule.
reactivity: A list of floating-point values that provide an estimate of the likelihood of the RNA backbone being cut at each nucleotide position. These values help determine the stability of the RNA structure under various experimental conditions.
errors: Arrays of floating-point numbers indicating the experimental errors corresponding to the measurements in the reactivity. These values help quantify the uncertainty in the degradation rates and reactivity measurements.

Variations

This dataset is available in two subsets:

License

This dataset is licensed under the AGPL-3.0 License.

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

Citation

@article{waymentsteele2022rna,
  author    = {Wayment-Steele, Hannah K and Kladwang, Wipapat and Strom, Alexandra I and Lee, Jeehyung and Treuille, Adrien and Becka, Alex and {Eterna Participants} and Das, Rhiju},
  journal   = {Nature Methods},
  month     = oct,
  number    = 10,
  pages     = {1234--1242},
  publisher = {Springer Science and Business Media LLC},
  title     = {{RNA} secondary structure packages evaluated and improved by high-throughput experiments},
  volume    = 19,
  year      = 2022
}