RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

Mariusz Popenda, Marta Szachniuk, Marek Blazewicz, Szymon Wasik, Edmund K Burke, Jacek Blazewicz, Ryszard W Adamiak
2010 BMC Bioinformatics  
Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first
more » ... b-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of threedimensional RNA fragments, their multi-parameter conformational analysis and visualization.
doi:10.1186/1471-2105-11-231 pmid:20459631 pmcid:PMC2873543 fatcat:2e6x7brd5vc7zcgso6trerwbui