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jgreener64 committed Nov 29, 2022
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# Progres - Protein Graph Embedding Search

This repository contains the method in the pre-print:
This repository contains the method from the pre-print:

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Greener JG and Jamali K. Fast protein structure searching using structure graph embeddings. bioRxiv (2022) - [link](https://www.biorxiv.org/content/10.1101/2022.11.28.518224v1)

It provides the `progres` Python package that lets you search structures against pre-embedded structural databases and pre-embed datasets for searching against. Searching typically takes 1-2 s and is faster for multiple queries. Currently [SCOPe](https://scop.berkeley.edu), [CATH](http://cathdb.info) and [ECOD](http://prodata.swmed.edu/ecod) are provided for searching against but we aim to add others such as the [AlphaFold database](https://alphafold.ebi.ac.uk) in future.

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