CoDNaS-RNA: a database of conformational diversity in the native state of RNA
Abstract Summary Conformational changes in RNA native ensembles are central to fulfill many of their biological roles. Systematic knowledge of the extent and possible modulators of this conformational diversity is desirable to better understand the relationship between RNA dynamics and function. We...
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| Veröffentlicht in: | Bioinformatics 2022-03, Vol.38 (6), p.1745-1748 |
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| container_title | Bioinformatics |
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| creator | González Buitrón, Martín Tunque Cahui, Ronaldo Romario García Ríos, Emilio Hirsh, Layla Parisi, Gustavo Fornasari, María Silvina Palopoli, Nicolas |
| description | Abstract
Summary
Conformational changes in RNA native ensembles are central to fulfill many of their biological roles. Systematic knowledge of the extent and possible modulators of this conformational diversity is desirable to better understand the relationship between RNA dynamics and function. We have developed CoDNaS-RNA as the first database of conformational diversity in RNA molecules. Known RNA structures are retrieved and clustered to identify alternative conformers of each molecule. Pairwise structural comparisons between all conformers within each cluster allows to measure the variability of the molecule. Additional annotations about structural features, molecular interactions and biological function are provided. All data in CoDNaS-RNA is free to download and available as a public website that can be of interest for researchers in computational biology and other life science disciplines.
Availability and implementation
The data underlying this article are available at http://ufq.unq.edu.ar/codnasrna or https://codnas-rna.bioinformatica.org/.
Supplementary information
Supplementary data are available at Bioinformatics online.
Graphical Abstract
Schematic workflow for data acquisition and processing to build CoDNaS-RNA |
| doi_str_mv | 10.1093/bioinformatics/btab858 |
| format | Article |
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Summary
Conformational changes in RNA native ensembles are central to fulfill many of their biological roles. Systematic knowledge of the extent and possible modulators of this conformational diversity is desirable to better understand the relationship between RNA dynamics and function. We have developed CoDNaS-RNA as the first database of conformational diversity in RNA molecules. Known RNA structures are retrieved and clustered to identify alternative conformers of each molecule. Pairwise structural comparisons between all conformers within each cluster allows to measure the variability of the molecule. Additional annotations about structural features, molecular interactions and biological function are provided. All data in CoDNaS-RNA is free to download and available as a public website that can be of interest for researchers in computational biology and other life science disciplines.
Availability and implementation
The data underlying this article are available at http://ufq.unq.edu.ar/codnasrna or https://codnas-rna.bioinformatica.org/.
Supplementary information
Supplementary data are available at Bioinformatics online.
Graphical Abstract
Schematic workflow for data acquisition and processing to build CoDNaS-RNA</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btab858</identifier><identifier>PMID: 34954795</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Computational Biology ; Molecular Conformation ; RNA ; Software</subject><ispartof>Bioinformatics, 2022-03, Vol.38 (6), p.1745-1748</ispartof><rights>The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2021</rights><rights>The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c401t-d2c8f502069ae98bf2e065b400a0e86f3fe4c21cf58ff9190bf6b142806279dd3</citedby><cites>FETCH-LOGICAL-c401t-d2c8f502069ae98bf2e065b400a0e86f3fe4c21cf58ff9190bf6b142806279dd3</cites><orcidid>0000-0001-7925-6436</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,1598,27903,27904</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bioinformatics/btab858$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34954795$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Valencia, Alfonso</contributor><creatorcontrib>González Buitrón, Martín</creatorcontrib><creatorcontrib>Tunque Cahui, Ronaldo Romario</creatorcontrib><creatorcontrib>García Ríos, Emilio</creatorcontrib><creatorcontrib>Hirsh, Layla</creatorcontrib><creatorcontrib>Parisi, Gustavo</creatorcontrib><creatorcontrib>Fornasari, María Silvina</creatorcontrib><creatorcontrib>Palopoli, Nicolas</creatorcontrib><title>CoDNaS-RNA: a database of conformational diversity in the native state of RNA</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract
Summary
Conformational changes in RNA native ensembles are central to fulfill many of their biological roles. Systematic knowledge of the extent and possible modulators of this conformational diversity is desirable to better understand the relationship between RNA dynamics and function. We have developed CoDNaS-RNA as the first database of conformational diversity in RNA molecules. Known RNA structures are retrieved and clustered to identify alternative conformers of each molecule. Pairwise structural comparisons between all conformers within each cluster allows to measure the variability of the molecule. Additional annotations about structural features, molecular interactions and biological function are provided. All data in CoDNaS-RNA is free to download and available as a public website that can be of interest for researchers in computational biology and other life science disciplines.
Availability and implementation
The data underlying this article are available at http://ufq.unq.edu.ar/codnasrna or https://codnas-rna.bioinformatica.org/.
Supplementary information
Supplementary data are available at Bioinformatics online.
Graphical Abstract
Schematic workflow for data acquisition and processing to build CoDNaS-RNA</description><subject>Computational Biology</subject><subject>Molecular Conformation</subject><subject>RNA</subject><subject>Software</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkF1LwzAUhoMobk7_wsilN3UnaZIm3o35CTrBj-uStAlW2mY26WD_3uo2wTuvzoHzvO-BB6EpgQsCKp2Zylet812jY1WEmYnaSC4P0JgwAQkFrg6HPRVZwiSkI3QSwgcAJ4yxYzRKmeIsU3yMHhf-aqlfkufl_BJrXOqhSAeLvcOF3z_wra5xWa1tF6q4wVWL47vF7XBZWxyijj_8UHGKjpyugz3bzQl6u7l-XdwlD0-394v5Q1IwIDEpaSEdBwpCaaukcdSC4IYBaLBSuNRZVlBSOC6dU0SBccIQRiUImqmyTCfofNu76vxnb0PMmyoUtq51a30fcioIy3jGUjagYosWnQ-hsy5fdVWju01OIP9Wmf9Vme9UDsHp7kdvGlv-xvbuBoBsAd-v_lv6BQs2hhM</recordid><startdate>20220304</startdate><enddate>20220304</enddate><creator>González Buitrón, Martín</creator><creator>Tunque Cahui, Ronaldo Romario</creator><creator>García Ríos, Emilio</creator><creator>Hirsh, Layla</creator><creator>Parisi, Gustavo</creator><creator>Fornasari, María Silvina</creator><creator>Palopoli, Nicolas</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-7925-6436</orcidid></search><sort><creationdate>20220304</creationdate><title>CoDNaS-RNA: a database of conformational diversity in the native state of RNA</title><author>González Buitrón, Martín ; Tunque Cahui, Ronaldo Romario ; García Ríos, Emilio ; Hirsh, Layla ; Parisi, Gustavo ; Fornasari, María Silvina ; Palopoli, Nicolas</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c401t-d2c8f502069ae98bf2e065b400a0e86f3fe4c21cf58ff9190bf6b142806279dd3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Computational Biology</topic><topic>Molecular Conformation</topic><topic>RNA</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>González Buitrón, Martín</creatorcontrib><creatorcontrib>Tunque Cahui, Ronaldo Romario</creatorcontrib><creatorcontrib>García Ríos, Emilio</creatorcontrib><creatorcontrib>Hirsh, Layla</creatorcontrib><creatorcontrib>Parisi, Gustavo</creatorcontrib><creatorcontrib>Fornasari, María Silvina</creatorcontrib><creatorcontrib>Palopoli, Nicolas</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>González Buitrón, Martín</au><au>Tunque Cahui, Ronaldo Romario</au><au>García Ríos, Emilio</au><au>Hirsh, Layla</au><au>Parisi, Gustavo</au><au>Fornasari, María Silvina</au><au>Palopoli, Nicolas</au><au>Valencia, Alfonso</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>CoDNaS-RNA: a database of conformational diversity in the native state of RNA</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2022-03-04</date><risdate>2022</risdate><volume>38</volume><issue>6</issue><spage>1745</spage><epage>1748</epage><pages>1745-1748</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract
Summary
Conformational changes in RNA native ensembles are central to fulfill many of their biological roles. Systematic knowledge of the extent and possible modulators of this conformational diversity is desirable to better understand the relationship between RNA dynamics and function. We have developed CoDNaS-RNA as the first database of conformational diversity in RNA molecules. Known RNA structures are retrieved and clustered to identify alternative conformers of each molecule. Pairwise structural comparisons between all conformers within each cluster allows to measure the variability of the molecule. Additional annotations about structural features, molecular interactions and biological function are provided. All data in CoDNaS-RNA is free to download and available as a public website that can be of interest for researchers in computational biology and other life science disciplines.
Availability and implementation
The data underlying this article are available at http://ufq.unq.edu.ar/codnasrna or https://codnas-rna.bioinformatica.org/.
Supplementary information
Supplementary data are available at Bioinformatics online.
Graphical Abstract
Schematic workflow for data acquisition and processing to build CoDNaS-RNA</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>34954795</pmid><doi>10.1093/bioinformatics/btab858</doi><tpages>4</tpages><orcidid>https://orcid.org/0000-0001-7925-6436</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Bioinformatics, 2022-03, Vol.38 (6), p.1745-1748 |
| issn | 1367-4803 1460-2059 1367-4811 |
| language | eng |
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| source | Oxford Journals Open Access Collection |
| subjects | Computational Biology Molecular Conformation RNA Software |
| title | CoDNaS-RNA: a database of conformational diversity in the native state of RNA |
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