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--- |
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dataset_info: |
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features: |
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- name: input_ids |
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sequence: int32 |
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- name: coords |
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sequence: |
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sequence: float64 |
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- name: labels |
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dtype: float64 |
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splits: |
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- name: train |
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num_bytes: 1434933392 |
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num_examples: 12479 |
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- name: val |
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num_bytes: 251648000 |
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num_examples: 4000 |
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- name: test |
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num_bytes: 249528000 |
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num_examples: 4000 |
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download_size: 718847118 |
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dataset_size: 1936109392 |
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configs: |
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- config_name: default |
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data_files: |
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- split: train |
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path: data/train-* |
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- split: val |
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path: data/val-* |
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- split: test |
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path: data/test-* |
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--- |
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# RSR: RNA Structure Ranking |
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## Overview |
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This task relates to predicting the three-dimensional structure of an RNA |
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molecule, given its sequence. A total of 21 RNAs are included, which consist of |
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the first 21 RNAs from the RNA-Puzzles competition (Cruz et al., 2011). |
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We phrase this problem as candidate ranking. For each RNA, we generate |
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candidate structural models using FARFAR2 (Watkins et al., 2020) and calculate |
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each candidate's atoms' root mean squared deviation (RMSD) to the experimentally |
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determined structure. |
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## Datasets |
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- splits: |
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- candidates-split-by-time: Oldest RNAs are in training set, next oldest are in validation, and newest are in testing set. |
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## Additional Information |
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The entry ['scores'] contains a dictionary with the following important entries: |
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- 'rms': RMSD from the experimentally determined structure. |
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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) |
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The ensemble denotes the |
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number of the RNA Puzzle, and the subunit denotes the index of the candidate |
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structural model. |
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## Citation Information |
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``` |
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@article{townshend2020atom3d, |
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title={Atom3d: Tasks on molecules in three dimensions}, |
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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}, |
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journal={arXiv preprint arXiv:2012.04035}, |
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year={2020} |
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} |
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``` |
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``` |
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@article{cruz2012rna, |
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title={RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction}, |
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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}, |
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journal={Rna}, |
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volume={18}, |
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number={4}, |
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pages={610--625}, |
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year={2012}, |
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publisher={Cold Spring Harbor Lab} |
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} |
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``` |
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``` |
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@article{watkins2020farfar2, |
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title={FARFAR2: improved de novo rosetta prediction of complex global RNA folds}, |
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author={Watkins, Andrew Martin and Rangan, Ramya and Das, Rhiju}, |
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journal={Structure}, |
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volume={28}, |
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number={8}, |
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pages={963--976}, |
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year={2020}, |
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publisher={Elsevier} |
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} |
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``` |
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