AtomGen
Collection
Suite of datasets and pre-trained models for molecular structures focusing on transformer-based implementations. • 10 items • Updated
Search is not available for this dataset
input_ids sequence | coords sequence | labels int64 |
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End of preview. Expand
in Data Studio
Residue identity prediction
Overview
Understanding the structural role of individual amino acids is important for engineering new proteins. We can understand this role by predicting the substitutabilities of different amino acids at a given protein site based on the surrounding structural environment. We generate a novel dataset consisting of atomic environments extracted from nonredundant structures in the PDB. We formulate this as a classification task where we predict the identity of the amino acid in the center of the environment based on all other atoms.
Datasets
- splits:
- split-by-cath-topology: split by CATH 4.2 topology class at the domain level (NOTE: only indices available for download currently due to size of dataset)
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}
}
- Downloads last month
- 96
Size of downloaded dataset files:
12.2 GB
Size of the auto-converted Parquet files:
12.2 GB
Number of rows:
4,661,580