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RUPEE: A fast and accurate purely geometric protein structure search

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...

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Detalles Bibliográficos
Autores principales: Ayoub, Ronald, Lee, Yugyung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420038/
https://www.ncbi.nlm.nih.gov/pubmed/30875409
http://dx.doi.org/10.1371/journal.pone.0213712
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author Ayoub, Ronald
Lee, Yugyung
author_facet Ayoub, Ronald
Lee, Yugyung
author_sort Ayoub, Ronald
collection PubMed
description 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. To address these limitations we have developed RUPEE, a fast and accurate 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 https://ayoubresearch.com. Code and data are available at https://github.com/rayoub/rupee.
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spelling pubmed-64200382019-04-02 RUPEE: A fast and accurate purely geometric protein structure search Ayoub, Ronald Lee, Yugyung PLoS One Research Article 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. To address these limitations we have developed RUPEE, a fast and accurate 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 https://ayoubresearch.com. Code and data are available at https://github.com/rayoub/rupee. Public Library of Science 2019-03-15 /pmc/articles/PMC6420038/ /pubmed/30875409 http://dx.doi.org/10.1371/journal.pone.0213712 Text en © 2019 Ayoub, Lee http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Ayoub, Ronald
Lee, Yugyung
RUPEE: A fast and accurate purely geometric protein structure search
title RUPEE: A fast and accurate purely geometric protein structure search
title_full RUPEE: A fast and accurate purely geometric protein structure search
title_fullStr RUPEE: A fast and accurate purely geometric protein structure search
title_full_unstemmed RUPEE: A fast and accurate purely geometric protein structure search
title_short RUPEE: A fast and accurate purely geometric protein structure search
title_sort rupee: a fast and accurate purely geometric protein structure search
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420038/
https://www.ncbi.nlm.nih.gov/pubmed/30875409
http://dx.doi.org/10.1371/journal.pone.0213712
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