Modeling RNA loops using sequence homology and geometric constraints

Summary: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion an...

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Detalles Bibliográficos
Autores principales: Schudoma, Christian, May, Patrick, Walther, Dirk
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887047/
https://www.ncbi.nlm.nih.gov/pubmed/20427516
http://dx.doi.org/10.1093/bioinformatics/btq236
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author Schudoma, Christian
May, Patrick
Walther, Dirk
author_facet Schudoma, Christian
May, Patrick
Walther, Dirk
author_sort Schudoma, Christian
collection PubMed
description Summary: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface. Availability and Implementation: The application was implemented in Python, MySQL and Apache. A web interface to the database and loop modeling application is freely available at http://rloom.mpimp-golm.mpg.de Contact: schudoma@mpimp-golm.mpg.de; may@mpimp-golm.mpg.de; walther@mpimp-golm.mpg.de
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spelling pubmed-28870472010-06-18 Modeling RNA loops using sequence homology and geometric constraints Schudoma, Christian May, Patrick Walther, Dirk Bioinformatics Applications Note Summary: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface. Availability and Implementation: The application was implemented in Python, MySQL and Apache. A web interface to the database and loop modeling application is freely available at http://rloom.mpimp-golm.mpg.de Contact: schudoma@mpimp-golm.mpg.de; may@mpimp-golm.mpg.de; walther@mpimp-golm.mpg.de Oxford University Press 2010-07-01 2010-04-28 /pmc/articles/PMC2887047/ /pubmed/20427516 http://dx.doi.org/10.1093/bioinformatics/btq236 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Schudoma, Christian
May, Patrick
Walther, Dirk
Modeling RNA loops using sequence homology and geometric constraints
title Modeling RNA loops using sequence homology and geometric constraints
title_full Modeling RNA loops using sequence homology and geometric constraints
title_fullStr Modeling RNA loops using sequence homology and geometric constraints
title_full_unstemmed Modeling RNA loops using sequence homology and geometric constraints
title_short Modeling RNA loops using sequence homology and geometric constraints
title_sort modeling rna loops using sequence homology and geometric constraints
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887047/
https://www.ncbi.nlm.nih.gov/pubmed/20427516
http://dx.doi.org/10.1093/bioinformatics/btq236
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