---
dataset_info:
  features:
  - name: input_ids
    sequence: int32
  - name: coords
    sequence:
      sequence: float64
  - name: labels
    dtype: float64
  splits:
  - name: train
    num_bytes: 1434933392
    num_examples: 12479
  - name: val
    num_bytes: 251648000
    num_examples: 4000
  - name: test
    num_bytes: 249528000
    num_examples: 4000
  download_size: 718847118
  dataset_size: 1936109392
configs:
- config_name: default
  data_files:
  - split: train
    path: data/train-*
  - split: val
    path: data/val-*
  - split: test
    path: data/test-*
---

# RSR: RNA Structure Ranking


## Overview

This task relates to predicting the three-dimensional structure of an RNA
molecule, given its sequence.  A total of 21 RNAs are included, which consist of
the first 21 RNAs from the RNA-Puzzles competition (Cruz et al., 2011).

We phrase this problem as candidate ranking.  For each RNA, we generate
candidate structural models using FARFAR2 (Watkins et al., 2020) and calculate
each candidate's atoms' root mean squared deviation (RMSD) to the experimentally
determined structure.

## Datasets

- splits:
   - candidates-split-by-time: Oldest RNAs are in training set, next oldest are in validation, and newest are in testing set.


## Additional Information

The entry ['labels'] contains the RMSD from the experimentally determined structure.

Many of the other scores are documented in [https://daslab.stanford.edu/site_data/pub_pdf/2017_Alford_JCTC.pdf](https://daslab.stanford.edu/site_data/pub_pdf/2017_Alford_JCTC.pdf)

The ensemble denotes the
number of the RNA Puzzle, and the subunit denotes the index of the candidate
structural model.

## Citation Information

```
@article{townshend2020atom3d,
  title={Atom3d: Tasks on molecules in three dimensions},
  author={Townshend, Raphael JL and V{\"o}gele, Martin and Suriana, Patricia and Derry, Alexander and Powers, Alexander and Laloudakis, Yianni and Balachandar, Sidhika and Jing, Bowen and Anderson, Brandon and Eismann, Stephan and others},
  journal={arXiv preprint arXiv:2012.04035},
  year={2020}
}
```

```
@article{cruz2012rna,
  title={RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction},
  author={Cruz, Jos{\'e} Almeida and Blanchet, Marc-Fr{\'e}d{\'e}rick and Boniecki, Michal and Bujnicki, Janusz M and Chen, Shi-Jie and Cao, Song and Das, Rhiju and Ding, Feng and Dokholyan, Nikolay V and Flores, Samuel Coulbourn and others},
  journal={Rna},
  volume={18},
  number={4},
  pages={610--625},
  year={2012},
  publisher={Cold Spring Harbor Lab}
}
```

```
@article{watkins2020farfar2,
  title={FARFAR2: improved de novo rosetta prediction of complex global RNA folds},
  author={Watkins, Andrew Martin and Rangan, Ramya and Das, Rhiju},
  journal={Structure},
  volume={28},
  number={8},
  pages={963--976},
  year={2020},
  publisher={Elsevier}
}
```