---
dataset_info:
  features:
  - name: input_ids
    sequence: int32
  - name: coords
    sequence:
      sequence: float64
  - name: labels
    sequence: float64
  splits:
  - name: train
    num_bytes: 1614130168
    num_examples: 25400
  - name: val
    num_bytes: 192093760
    num_examples: 2800
  - name: test
    num_bytes: 1264620360
    num_examples: 16014
  download_size: 1497041025
  dataset_size: 3070844288
configs:
- config_name: default
  data_files:
  - split: train
    path: data/train-*
  - split: val
    path: data/val-*
  - 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}
}
```