|
--- |
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dataset_info: |
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features: |
|
- name: input_ids |
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sequence: int32 |
|
- name: coords |
|
sequence: |
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sequence: float64 |
|
- name: labels |
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sequence: float64 |
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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 |
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data_files: |
|
- split: train |
|
path: data/train-* |
|
- split: val |
|
path: data/val-* |
|
- split: test |
|
path: data/test-* |
|
--- |
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|
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# PSR: Protein Structure Ranking |
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|
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## Overview |
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|
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This task relates to predicting the three-dimensional structure of a protein |
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molecule, given its sequence. A total of around 700 protein targets are included, |
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which consist of protein targets from Critical Assessment of Structure |
|
Prediction (CASP) 5-13. |
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|
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We phrase this problem as decoy ranking. For each protein target, we |
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include its decoys sets compiled from the CASP decoy sets released for the |
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Model Quality Assessment (MQA). We relax those structures with the SCWRL4 |
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software (Krivov and Dunbrack, 2019) to improve side-chain conformations. For |
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each decoy, we calculate the RMSD, TM-score, GDT_TS, and GDT_HA scores to the |
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experimentally determined structure using the TM-score software (Zhang and |
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Skolnick, 2007). |
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|
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## Datasets |
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- splits: |
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- split-by-year: This dataset contains data in the CASP dataset, but is split |
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temporally. More specifically, we randomly split the targets in CASP5-10 and |
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randomly sample 50 decoys for each target to generate the training and validation |
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sets (508 targets for training, 56 targets for validation), and use the CASP11 |
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Stage 2 as test set (85 targets total, with 150 decoys for each target, excluding |
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the native structures). |
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|
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## Citation Information |
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|
|
``` |
|
@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} |
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} |
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``` |
|
|
|
``` |
|
@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}, |
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journal={Proteins: Structure, Function, and Bioinformatics}, |
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volume={87}, |
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number={12}, |
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pages={1011--1020}, |
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year={2019}, |
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publisher={Wiley Online Library} |
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} |
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``` |
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|
|
|
