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---
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}
}
```
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