proteinsdataset's Introduction

Protein Datasets

We collect three protein datasets: ProteinsDBDataset, HomologyTAPEDataset and ProtFunctDataset, from https://github.com/phermosilla/IEConv_proteins, and convert them to PyG datasets.

Statistics

Dataset	# of graphs	Splitting
`ProteinsDBDataset`	1,178	Use 10-fold cross validation
`HomologyTAPEDataset`	16,292	training:validation:test_fold:test_family:test_superfamily = 12312:736:718:1272:1254
`ProtFunctDataset`	37,428	training:validation:testing = 29215:2562:5651

Dataset	Average # of nodes	Average # of edges
`ProteinsDBDataset`	475.9	1,483.7
`HomologyTAPEDataset`	167.3	513.5
`ProtFunctDataset`	298.5	929.1

Usage

Processing the datasets require the IEProtLib.py_utils.py_mol package, which can be obtained by cloning https://github.com/phermosilla/IEConv_proteins and copy the IEProtLib/py_utils/py_mol directory in that repo to the root directory of this repo.

ProteinsDBDataset:

https://drive.google.com/uc?export=download&id=1KTs5cUYhG60C6WagFp4Pg8xeMgvbLfhB

Extract content in: [root]/raw/ProteinsDB/

HomologyTAPEDataset:

https://drive.google.com/uc?export=download&id=1chZAkaZlEBaOcjHQ3OUOdiKZqIn36qar

Extract content in: [root]/raw/HomologyTAPE/

ProtFunctDataset:

https://drive.google.com/uc?export=download&id=1udP6_90WYkwkvL1LwqIAzf9ibegBJ8rI

Extract content in: [root]/raw/ProtFunct/

NOTICE that all three datasets contain directed graphs, although only a small portion of the edges are single-directed. We provide a simple helper method utils.to_undirected() to convert a graph to undirected by adding inverse edges.

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