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RUPEE: A fast and accurate purely geometric protein structure search

View ORCID ProfileRonald Ayoub, Yugyung Lee
doi: https://doi.org/10.1101/475301
Ronald Ayoub
1School of Computing and Engineering, University of Missouri at Kansas City, USA
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Yugyung Lee
1School of Computing and Engineering, University of Missouri at Kansas City, USA
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Abstract

Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results. These limitations can prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. We have developed RUPEE, a fast, scalable, and purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles.

Comparing our results to the output of mTM, SSM, and the CATHEDRAL structural scan, it is clear that RUPEE has set a new bar for purely geometric big data approaches to protein structure searches. RUPEE in top-aligned mode produces equal or better results than the best available protein structure searches, and RUPEE in fast mode demonstrates the fastest response times coupled with high quality results.

The RUPEE protein structure search is available at http://www.ayoubresearch.com. Code and data are available at https://github.com/rayoub/rupee.

Footnotes

  • ↵* ronaldayoub{at}mail.umkc.edu

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 November 20, 2018.
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RUPEE: A fast and accurate purely geometric protein structure search
Ronald Ayoub, Yugyung Lee
bioRxiv 475301; doi: https://doi.org/10.1101/475301
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RUPEE: A fast and accurate purely geometric protein structure search
Ronald Ayoub, Yugyung Lee
bioRxiv 475301; doi: https://doi.org/10.1101/475301

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