{"id":21280599,"url":"https://github.com/borgwardtlab/proteinshake","last_synced_at":"2025-07-11T10:32:23.024Z","repository":{"id":41414889,"uuid":"507042456","full_name":"BorgwardtLab/proteinshake","owner":"BorgwardtLab","description":"Protein structure datasets for machine 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align=\"center\"\u003e\u003cb\u003e\u003ci\u003e\nImportant note: ProteinShake has broadened its scope and is continued in other repositories\n\u003c/i\u003e\u003c/b\u003e\u003c/p\u003e\n\u003cp align=\"center\"\u003e\u003cb\u003e\u003ci\u003e\nCheck out our latest work on the \u003ca href=\"https://www.bioverse.rsvp\"\u003ebioverse\u003c/a\u003e (all biomolecules) and \u003ca href=\"https://rnaglib.org\"\u003ernaglib\u003c/a\u003e (for RNA)\n\nWe will continue to maintain existing functionality in this repository, please submit issues or PRs with any bugs or suggestions.\n\u003c/i\u003e\u003c/b\u003e\u003c/p\u003e\n\n---\n\n\u003cp align=\"center\"\u003e\n\u003cimg src=\"https://raw.githubusercontent.com/BorgwardtLab/proteinshake/main/docs/images/logo_subtitle.png#gh-light-mode-only\" width=\"60%\"\u003e\n\u003c/p\u003e\n\u003cp align=\"center\"\u003e\n\u003cimg src=\"https://raw.githubusercontent.com/BorgwardtLab/proteinshake/main/docs/images/logo_subtitle_dark.png#gh-dark-mode-only\" width=\"60%\"\u003e\n\u003c/p\u003e\n\n\u003cdiv align=\"center\"\u003e\n\n![build](https://img.shields.io/github/actions/workflow/status/borgwardtlab/proteinshake/build.yml?color=%2303A9F4\u0026style=for-the-badge)\n[![pypi](https://img.shields.io/pypi/v/proteinshake?color=%2303A9F4\u0026style=for-the-badge)](https://pypi.org/project/proteinshake/)\n[![docs](https://img.shields.io/readthedocs/proteinshake?color=%2303A9F4\u0026style=for-the-badge)](https://proteinshake.readthedocs.io/en/latest/?badge=latest)\n[![downloads](https://img.shields.io/pypi/dm/proteinshake?color=%2303A9F4\u0026style=for-the-badge)](https://pypi.org/project/proteinshake/)\n[![codecov](https://img.shields.io/codecov/c/gh/BorgwardtLab/proteinshake?color=%2303A9F4\u0026style=for-the-badge\u0026token=0NL6CQZ6MB)](https://codecov.io/gh/BorgwardtLab/proteinshake)\n\u003c/div\u003e\n\n\u003cp align=\"center\"\u003e\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\n\u003ca href=\"https://borgwardtlab.github.io/proteinshake/#quickstart\"\u003eQuickstart\u003c/a\u003e\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\n\u003ca href=\"https://borgwardtlab.github.io/proteinshake\"\u003eWebsite\u003c/a\u003e\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\n\u003ca href=\"https://proteinshake.readthedocs.io/en/latest/?badge=latest\"\u003eDocumentation\u003c/a\u003e\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\n\u003ca href=\"https://proceedings.neurips.cc/paper_files/paper/2023/file/b6167294ed3d6fc61e11e1592ce5cb77-Paper-Datasets_and_Benchmarks.pdf\"\u003ePaper\u003c/a\u003e\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\n\u003ca href=\"https://proteinshake.readthedocs.io/en/latest/notes/contribution.html\"\u003eContribute\u003c/a\u003e\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\n\u003ca href=\"https://borgwardtlab.github.io/proteinshake/#leaderboard\"\u003eLeaderboard\u003c/a\u003e\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\n\u003ca href=\"https://proteinshake.readthedocs.io/en/latest/notebooks/dataset.html\"\u003eTutorials\u003c/a\u003e\n\u003c/p\u003e\n\n\u003cdiv align=\"center\"\u003e\n\n### ProteinShake provides one-liner imports of large scale, preprocessed protein structure datasets and tasks for various model types and frameworks.\n\nWe 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.\n\nFind more information on the \u003ca href=\"https://borgwardtlab.github.io/proteinshake\"\u003eWebsite\u003c/a\u003e and the \u003ca href=\"https://proteinshake.readthedocs.io/en/latest/?badge=latest\"\u003eDocumentation\u003c/a\u003e, or check out the \u003ca href=\"https://proteinshake.readthedocs.io/en/latest/notebooks/dataset.html\"\u003eTutorials\u003c/a\u003e. The results of the paper and the baseline models can be found in the \u003ca href=\"https://github.com/BorgwardtLab/ProteinShake_eval\"\u003eEvaluation Repository\u003c/a\u003e. If you would like to create your own release, see the \u003ca href=\"https://github.com/BorgwardtLab/proteinshake_release\"\u003eRelease Repository\u003c/a\u003e.\n\n\u003c/br\u003e\n\n\n  \n**Installation:**\n\n\n\u003cdiv align=\"center\"\u003e\n  \n```\npip install proteinshake\n```\n\n\u003c/div\u003e\n\n\u003c/br\u003e\n\n\u003cdiv align=\"center\"\u003e\n\n*Code in this repository is licensed under [BSD-3](https://github.com/BorgwardtLab/proteinshake/blob/main/LICENSE), the dataset files on Zenodo are licensed under [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/legalcode).*\n\n*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.*\n\n\u003c/div\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fborgwardtlab%2Fproteinshake","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fborgwardtlab%2Fproteinshake","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fborgwardtlab%2Fproteinshake/lists"}