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---
dataset_info:
features:
- name: input_ids
sequence: int32
- name: coords
sequence:
sequence: float64
- name: labels
dtype: int64
- name: token_type_ids
sequence: int8
splits:
- name: train
num_bytes: 7068868047
num_examples: 87303
- name: val
num_bytes: 2279753092
num_examples: 31050
- name: test
num_bytes: 1213864413
num_examples: 15268
download_size: 4100975348
dataset_size: 10562485552
configs:
- config_name: default
data_files:
- split: train
path: data/train-*
- split: val
path: data/val-*
- split: test
path: data/test-*
---
# PPI: Protein-Protein Interfaces
## Overview
This task relates to predicting which pairs of amino acids, spanning two
different proteins, will interact upon binding (when they form a complex).
Amino acids are defined as interacting if any of their heavy atoms are within 6
Angstroms from one another.
## Datasets
- splits:
- DIPS-split: DIPS dataset, split by sequence identity (see add. inf.)
## Format
Each entry in the dataset contains the following keys:
- ['input_ids'] The set of atomic numbers for both the proteins in the complex concatenated together.
- ['coords'] The 3D coordinates for both the proteins in the complex concatenated together.
- ['label'] 1 for interacting, 0 for not interacting.
- ['token_type_ids'] A mask that corresponds to which inputs_ids/coords belong to the two individual proteins involved in the complex (0 for protein 1 , 1 for protein 2)
## Additional Information
The ensemble consists of a given protein complex, with subunits corresponding
to the two individual proteins involved in the complex.
## 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{paszke2019advances,
title={Advances in neural information processing systems 32},
author={Paszke, Adam and Gross, Sam and Massa, Francisco and Lerer, Adam and Bradbury, James and Chanan, Gregory and Killeen, Trevor and Lin, Zeming and Gimelshein, Natalia and Antiga, Luca and others},
journal={Curran Associates, Inc},
pages={8024--8035},
year={2019}
}
```
```
@article{vreven2015updates,
title={Updates to the integrated protein--protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2},
author={Vreven, Thom and Moal, Iain H and Vangone, Anna and Pierce, Brian G and Kastritis, Panagiotis L and Torchala, Mieczyslaw and Chaleil, Raphael and Jim{\'e}nez-Garc{\'\i}a, Brian and Bates, Paul A and Fernandez-Recio, Juan and others},
journal={Journal of molecular biology},
volume={427},
number={19},
pages={3031--3041},
year={2015},
publisher={Elsevier}
}
```
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