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RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs
In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee—a new tool that allows to extract RNA secon...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086112/ https://www.ncbi.nlm.nih.gov/pubmed/24771339 http://dx.doi.org/10.1093/nar/gku330 |
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author | Antczak, Maciej Zok, Tomasz Popenda, Mariusz Lukasiak, Piotr Adamiak, Ryszard W. Blazewicz, Jacek Szachniuk, Marta |
author_facet | Antczak, Maciej Zok, Tomasz Popenda, Mariusz Lukasiak, Piotr Adamiak, Ryszard W. Blazewicz, Jacek Szachniuk, Marta |
author_sort | Antczak, Maciej |
collection | PubMed |
description | In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee—a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/. |
format | Online Article Text |
id | pubmed-4086112 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-40861122014-12-02 RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs Antczak, Maciej Zok, Tomasz Popenda, Mariusz Lukasiak, Piotr Adamiak, Ryszard W. Blazewicz, Jacek Szachniuk, Marta Nucleic Acids Res Article In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee—a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/. Oxford University Press 2014-07-01 2014-04-25 /pmc/articles/PMC4086112/ /pubmed/24771339 http://dx.doi.org/10.1093/nar/gku330 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Article Antczak, Maciej Zok, Tomasz Popenda, Mariusz Lukasiak, Piotr Adamiak, Ryszard W. Blazewicz, Jacek Szachniuk, Marta RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs |
title | RNApdbee—a webserver to derive secondary structures from pdb
files of knotted and unknotted RNAs |
title_full | RNApdbee—a webserver to derive secondary structures from pdb
files of knotted and unknotted RNAs |
title_fullStr | RNApdbee—a webserver to derive secondary structures from pdb
files of knotted and unknotted RNAs |
title_full_unstemmed | RNApdbee—a webserver to derive secondary structures from pdb
files of knotted and unknotted RNAs |
title_short | RNApdbee—a webserver to derive secondary structures from pdb
files of knotted and unknotted RNAs |
title_sort | rnapdbee—a webserver to derive secondary structures from pdb
files of knotted and unknotted rnas |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086112/ https://www.ncbi.nlm.nih.gov/pubmed/24771339 http://dx.doi.org/10.1093/nar/gku330 |
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