proteinshake 0.0.2

Deep learning ready datasets of 3D protein structures.

proteinshake: the largest repository of ML-ready protein 3D structure datasets

This is a collection of torch-geometric datasets built from PDB and AlphaFold. After installing, datasets can be passed directly to ML loaders for model training.

name	num_proteins	avg size (# residues)	property	values	type
RCSBDataset	21989	56.8898	-	-	-
PfamDataset	18696	59.4297	Protein Family (Pfam)	5215 (root)	Categorical, Hierarchical
GODataset	19267	58.8485	Gene Ontology (GO)	101 (root)	Categorical, Hierarchical
ECDataset	8150	74.9618	Enzyme Classification (EC)	2173	Categorical
PDBBindRefined	4642	108.806	Small Mol. Binding Site (residue-level)	2	Binary
TMScoreBenchmark	200	49.458	TM Score	[0-1]	Real-valued, Pairwise
AlphaFoldDataset_arabidopsis_thaliana	27434	66.1312	-	-	-
AlphaFoldDataset_caenorhabditis_elegans	19694	65.0678	-	-	-
AlphaFoldDataset_candida_albicans	5974	62.782	-	-	-
AlphaFoldDataset_danio_rerio	24664	75.2797	-	-	-
AlphaFoldDataset_dictyostelium_discoideum	12622	85.9275	-	-	-
AlphaFoldDataset_drosophila_melanogaster	13458	81.2947	-	-	-
AlphaFoldDataset_escherichia_coli	4363	51.5408	-	-	-
AlphaFoldDataset_glycine_max	55799	58.0664	-	-	-
AlphaFoldDataset_homo_sapiens	23391	105.457	-	-	-
AlphaFoldDataset_methanocaldococcus_jannaschii	1773	46.7467	-	-	-
AlphaFoldDataset_mus_musculus	21615	83.0434	-	-	-
AlphaFoldDataset_oryza_sativa	43649	44.1931	-	-	-
AlphaFoldDataset_rattus_norvegicus	21272	78.1547	-	-	-
AlphaFoldDataset_saccharomyces_cerevisiae	6040	80.0745	-	-	-
AlphaFoldDataset_schizosaccharomyces_pombe	5128	76.2427	-	-	-
AlphaFoldDataset_zea_mays	39299	46.1618	-	-	-

Installation

$ pip install proteinshake

Note: ensure that you are using the correct versions of torch-[scatter,sparse] according to your hardware and cuda version. See this page for more info.

From source

$ git clone https://github.com/BorgwardtLab/proteinshake
$ cd proteinshake
$ pip install .

Usage

See the quickstart guide on our documentation site to get started.

Licenses

We make our code available under the MIT License. The datasets are distributed under CC-BY-4.0.

We obtained and modified data from the following sources:

The AlphaFold protein structures were downloaded from the AlphaFold Structure Database, licensed under CC-BY-4.0.

The RCSB protein structures were downloaded from RCSB, licensed under CC0 1.0.