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ProteinShake: Building datasets and benchmarks for deep learning on protein structures

We present ProteinShake, a Python software package that simplifies dataset creation and model evaluation for deep learning on protein structures. Users can create custom datasets or load an extensive set of pre-processed datasets from the Protein Data Bank (PDB) and AlphaFoldDB. Each dataset is associated with prediction tasks and evaluation functions covering a broad array of biological challenges. A benchmark on these tasks shows that pre-training almost always improves performance, the optimal data modality (graphs, voxel grids, or point clouds) is task-dependent, and models struggle to generalize to new structures. ProteinShake makes protein structure data easily accessible and comparison among models straightforward, providing challenging benchmark settings with real-world implications. ProteinShake is available at: https://proteinshake.ai

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