proteinshake 0.1.0

Deep learning ready datasets of 3D protein structures.

ML-ready protein 3D structure datasets

• Fetch clean protein datasets in one line
• Convert proteins to graphs, point clouds, voxels, and surfaces (coming soon).
• Work in your favorite deep learning framework (pytorch, tensorflow, pytorch-geometric, dgl, networkx)

proteinshake is a collection of protein structure datasets built from PDB and AlphaFold. After installing, datasets can be passed directly to ML loaders for model training.

PDB Datasets

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

AlphaFold Datasets

name	num_proteins	avg size (# residues)	property	values	type
SwissProt	512.231	79.334	-	-	-
arabidopsis_thaliana	27434	66.1312	-	-	-
caenorhabditis_elegans	19694	65.0678	-	-	-
candida_albicans	5974	62.782	-	-	-
danio_rerio	24664	75.2797	-	-	-
dictyostelium_discoideum	12622	85.9275	-	-	-
drosophila_melanogaster	13458	81.2947	-	-	-
escherichia_coli	4363	51.5408	-	-	-
glycine_max	55799	58.0664	-	-	-
homo_sapiens	23391	105.457	-	-	-
methanocaldococcus_jannaschii	1773	46.7467	-	-	-
mus_musculus	21615	83.0434	-	-	-
oryza_sativa	43649	44.1931	-	-	-
rattus_norvegicus	21272	78.1547	-	-	-
saccharomyces_cerevisiae	6040	80.0745	-	-	-
schizosaccharomyces_pombe	5128	76.2427	-	-	-
zea_mays	39299	46.1618	-	-	-

Installation

$ pip install proteinshake

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.

Legal Note

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.