vector-institute/atom3d-ppi

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}
}