Modeling RNA loops using sequence homology and geometric constraints.
CONCLUSIONS
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.


METHODS
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


BACKGROUND
schudoma@mpimp-golm.mpg.de; may@mpimp-golm.mpg.de; walther@mpimp-golm.mpg.de
Schudoma
Christian
C
Bioinformatics Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany. schudoma@mpimp-golm.mpg.de
May
Patrick
P
Walther
Dirk
D
D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
D012313:RNA