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--- |
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dataset_info: |
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features: |
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- name: input_ids |
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sequence: int32 |
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- name: coords |
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sequence: |
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sequence: float64 |
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- name: labels |
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dtype: int64 |
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- name: token_type_ids |
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sequence: int8 |
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splits: |
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- name: train |
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num_bytes: 7068868047 |
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num_examples: 87303 |
|
- name: val |
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num_bytes: 2279753092 |
|
num_examples: 31050 |
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- name: test |
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num_bytes: 1213864413 |
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num_examples: 15268 |
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download_size: 4100975348 |
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dataset_size: 10562485552 |
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configs: |
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- config_name: default |
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data_files: |
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- split: train |
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path: data/train-* |
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- split: val |
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path: data/val-* |
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- split: test |
|
path: data/test-* |
|
--- |
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# PPI: Protein-Protein Interfaces |
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## Overview |
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This task relates to predicting which pairs of amino acids, spanning two |
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different proteins, will interact upon binding (when they form a complex). |
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Amino acids are defined as interacting if any of their heavy atoms are within 6 |
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Angstroms from one another. |
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## Datasets |
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- splits: |
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- DIPS-split: DIPS dataset, split by sequence identity (see add. inf.) |
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## Format |
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Each entry in the dataset contains the following keys: |
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- ['input_ids'] The set of atomic numbers for both the proteins in the complex concatenated together. |
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- ['coords'] The 3D coordinates for both the proteins in the complex concatenated together. |
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- ['label'] 1 for interacting, 0 for not interacting. |
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- ['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) |
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## Additional Information |
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The ensemble consists of a given protein complex, with subunits corresponding |
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to the two individual proteins involved in the complex. |
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## Citation Information |
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|
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``` |
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@article{townshend2020atom3d, |
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title={Atom3d: Tasks on molecules in three dimensions}, |
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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}, |
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journal={arXiv preprint arXiv:2012.04035}, |
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year={2020} |
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} |
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``` |
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|
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``` |
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@article{paszke2019advances, |
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title={Advances in neural information processing systems 32}, |
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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}, |
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journal={Curran Associates, Inc}, |
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pages={8024--8035}, |
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year={2019} |
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} |
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``` |
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|
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``` |
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@article{vreven2015updates, |
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title={Updates to the integrated protein--protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2}, |
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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}, |
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journal={Journal of molecular biology}, |
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volume={427}, |
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number={19}, |
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pages={3031--3041}, |
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year={2015}, |
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publisher={Elsevier} |
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} |
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``` |
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