Update README.md

README.md

@@ -30,3 +30,71 @@ configs:
   - 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 ['scores'] contains a dictionary with the following important entries:
+- 'rms': 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}
+}
+```