Introduced by Townshend et al. in ATOM3D: Tasks On Molecules in Three Dimensions

ATOM3D is a unified collection of datasets concerning the three-dimensional structure of biomolecules, including proteins, small molecules, and nucleic acids. These datasets are specifically designed to provide a benchmark for machine learning methods which operate on 3D molecular structure, and represent a variety of important structural, functional, and engineering tasks. All datasets are provided in a standardized format along with a Python package containing processing code, utilities, models, and dataloaders for common machine learning frameworks such as PyTorch. ATOM3D is designed to be a living database, where datasets are updated and tasks are added as the field progresses.

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