Update README.md

README.md

@@ -30,3 +30,56 @@ configs:
   - split: test
     path: data/test-*
 ---
+
+# PSR: Protein Structure Ranking
+
+
+## Overview
+
+This task relates to predicting the three-dimensional structure of a protein
+molecule, given its sequence. A total of around 700 protein targets are included,
+which consist of protein targets from Critical Assessment of Structure
+Prediction (CASP) 5-13.
+
+We phrase this problem as decoy ranking. For each protein target, we
+include its decoys sets compiled from the CASP decoy sets released for the
+Model Quality Assessment (MQA). We relax those structures with the SCWRL4
+software (Krivov and Dunbrack, 2019) to improve side-chain conformations. For
+each decoy, we calculate the RMSD, TM-score, GDT_TS, and GDT_HA scores to the
+experimentally determined structure using the TM-score software (Zhang and
+Skolnick, 2007).
+
+
+## Datasets
+- splits:
+   - split-by-year: This dataset contains data in the CASP dataset, but is split 
+   temporally. More specifically, we randomly split the targets in CASP5-10 and 
+   randomly sample 50 decoys for each target to generate the training and validation 
+   sets (508 targets for training, 56 targets for validation), and use the CASP11 
+   Stage 2 as test set (85 targets total, with 150 decoys for each target, excluding
+   the native structures). 
+
+## 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{kryshtafovych2019critical,
+  title={Critical assessment of methods of protein structure prediction (CASP)—Round XIII},
+  author={Kryshtafovych, Andriy and Schwede, Torsten and Topf, Maya and Fidelis, Krzysztof and Moult, John},
+  journal={Proteins: Structure, Function, and Bioinformatics},
+  volume={87},
+  number={12},
+  pages={1011--1020},
+  year={2019},
+  publisher={Wiley Online Library}
+}
+```
+