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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2019
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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. |
format | Online Article Text |
id | pubmed-6420038 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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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