Modeling RNA loops using sequence homology and geometric constraints.
basic_science · Level V
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- Record sourced from PubMed, PMID 20427516.
- Also identified by DOI 10.1093/bioinformatics/btq236 and PMC identifier 2887047.
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Abstract
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. 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 schudoma@mpimp-golm.mpg.de; may@mpimp-golm.mpg.de; walther@mpimp-golm.mpg.de
Medical subject headings
- Models, Chemical
- Nucleic Acid Conformation
- RNA
- Sequence Homology, Nucleic Acid
- Software