Quickstart      Website      Documentation      Paper      Contribute      Leaderboard      Tutorials

ProteinShake provides one-liner imports of large scale, preprocessed protein structure datasets and tasks for various model types and frameworks.

!!! THIS IS A DEVELOPMENT FORK !!! DO NOT USE !!!

We provide a collection of preprocessed and cleaned protein 3D structure datasets from RCSB and AlphaFoldDB, including annotations. Structures are easily converted to graphs, voxels, or point clouds and loaded natively into PyTorch, TensorFlow, NumPy, JAX, PyTorch Geometric, DGL and NetworkX. The task API enables standardized benchmarking on a variety of tasks on protein and residue level.

!!! THIS IS A DEVELOPMENT FORK !!! DO NOT USE !!!

Installation:

pip install proteinshake

Code in this repository is licensed under BSD-3, the dataset files on Zenodo are licensed under CC-BY-4.0.

To build ProteinShake, we obtained and modified data from various sources. Please see the documentation of the respective dataset classes for a reference to the original data, license, and paper.