AtomGen
Collection
Suite of datasets and pre-trained models for molecular structures focusing on transformer-based implementations. • 10 items • Updated
Search is not available for this dataset
input_ids sequencelengths 1.47k 6.03k | coords sequencelengths 1.47k 6.04k | labels float64 1.93 56.1 |
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... | [
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... | 32.695 |
[6,6,8,6,8,6,6,8,7,6,8,7,6,8,6,6,1,1,1,1,1,1,1,1,15,8,8,8,6,6,8,6,8,6,6,8,7,6,7,7,6,6,6,8,7,6,7,1,1,(...TRUNCATED) | [[32.450001,94.236,265.070007],[30.959999,94.366997,264.893005],[30.483,95.584,265.526001],[30.54700(...TRUNCATED) | 22.367 |
[6,6,8,6,8,6,6,8,7,6,8,7,6,8,6,6,1,1,1,1,1,1,1,1,15,8,8,8,6,6,8,6,8,6,6,8,7,6,7,7,6,6,6,8,7,6,7,1,1,(...TRUNCATED) | [[11.094,71.683998,261.105011],[12.355,71.138,260.487],[12.036,70.070999,259.553986],[13.108,72.1740(...TRUNCATED) | 21.355 |
[6,6,8,6,8,6,6,8,7,6,8,7,6,8,6,6,1,1,1,1,1,1,1,1,15,8,8,8,6,6,8,6,8,6,6,8,7,6,7,7,6,6,6,8,7,6,7,1,1,(...TRUNCATED) | [[10.864,130.369995,243.376007],[10.722,128.992004,243.968002],[9.378,128.487,243.748001],[11.645,12(...TRUNCATED) | 33.286 |
[6,6,8,6,8,6,6,8,7,6,8,7,6,8,6,6,1,1,1,1,1,1,1,1,15,8,8,8,6,6,8,6,8,6,6,8,7,6,7,7,6,6,6,8,7,6,7,1,1,(...TRUNCATED) | [[15.72,122.787003,251.751999],[17.176001,122.399002,251.778],[17.358999,121.184998,252.554001],[17.(...TRUNCATED) | 31.296 |
[6,6,8,6,8,6,6,8,7,6,8,7,6,8,6,6,1,1,1,1,1,1,1,1,15,8,8,8,6,6,8,6,8,6,6,8,7,6,7,7,6,6,6,8,7,6,7,1,1,(...TRUNCATED) | [[14.115,101.113998,266.536987],[13.281,102.024002,265.673004],[13.901,103.333,265.575012],[13.156,1(...TRUNCATED) | 18.242 |
[6,6,8,6,8,6,6,8,7,6,8,7,6,8,6,6,1,1,1,1,1,1,1,1,15,8,8,8,6,6,8,6,8,6,6,8,7,6,7,7,6,6,6,8,7,6,7,1,1,(...TRUNCATED) | [[35.325001,93.285004,181.785995],[36.231998,92.460999,182.662994],[37.570999,93.022003,182.669006],(...TRUNCATED) | 31.307 |
[6,6,8,6,8,6,6,8,7,6,8,7,6,8,6,6,1,1,1,1,1,1,1,1,15,8,8,8,6,6,8,6,8,6,6,8,7,6,7,7,6,6,6,8,7,6,7,1,1,(...TRUNCATED) | [[46.388,105.509003,258.648987],[45.473999,104.333,258.876007],[44.43,104.682999,259.822998],[44.745(...TRUNCATED) | 19.107 |
[6,6,8,6,8,6,6,8,7,6,8,7,6,8,6,6,1,1,1,1,1,1,1,1,15,8,8,8,6,6,8,6,8,6,6,8,7,6,7,7,6,6,6,8,7,6,7,1,1,(...TRUNCATED) | [[8.469,77.278,239.072998],[8.971,77.472,237.666],[8.043,78.293999,236.908997],[10.298,78.207001,237(...TRUNCATED) | 21.649 |
[6,6,8,6,8,6,6,8,7,6,8,7,6,8,6,6,1,1,1,1,1,1,1,1,15,8,8,8,6,6,8,6,8,6,6,8,7,6,7,7,6,6,6,8,7,6,7,1,1,(...TRUNCATED) | [[6.818,78.653999,254.723007],[6.837,78.224998,253.278],[5.605,78.622002,252.619995],[7.949,78.88400(...TRUNCATED) | 20.444 |
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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
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}
}
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