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Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures

View ORCID ProfileArian R. Jamasb, Pietro Lió, Tom L. Blundell
doi: https://doi.org/10.1101/2020.07.15.204701
Arian R. Jamasb
1Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
2Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
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  • ORCID record for Arian R. Jamasb
  • For correspondence: arj39@cam.ac.uk
Pietro Lió
2Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
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Tom L. Blundell
1Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Abstract

Graphein is a python library for constructing graph and surface-mesh representations of protein structures for computational analysis. The library interfaces with popular geometric deep learning libraries: DGL, PyTorch Geometric and PyTorch3D. Geometric deep learning is emerging as a popular methodology in computational structural biology. As feature engineering is a vital step in a machine learning project, the library is designed to be highly flexible, allowing the user to parameterise the graph construction, scaleable to facilitate working with large protein complexes, and containing useful pre-processing tools for preparing experimental structure files. Graphein is also designed to facilitate network-based and graph-theoretic analyses of protein structures in a high-throughput manner. As example workflows, we make available two new protein structure-related datasets, previously unused by the geometric deep learning community.

Availability and implementation Graphein is written in python. Source code, example usage and datasets, and documentation are made freely available under a MIT License at the following URL: https://github.com/a-r-j/graphein

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 15, 2020.
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Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures
Arian R. Jamasb, Pietro Lió, Tom L. Blundell
bioRxiv 2020.07.15.204701; doi: https://doi.org/10.1101/2020.07.15.204701
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Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures
Arian R. Jamasb, Pietro Lió, Tom L. Blundell
bioRxiv 2020.07.15.204701; doi: https://doi.org/10.1101/2020.07.15.204701

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