Abstract
The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA–protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/
Highlights
RNA seems to be the least investigated class of irregular biopolymers
The database web interface is developed as a collection of Python 2.7 CGI scripts along with HTML pages and JavaScript code
Universe of RNA Structures DataBase (URSDB) is a relational database powered by MySQL server
Summary
The role of the messenger, transfer and ribosomal RNA is well known, but the role of various non-coding RNA in the regulation of intracellular processes, including the regulation of gene expression, requires further study, see the review [1]. Until recently RNA structures were mostly studied from the perspective of pseudoknot-free RNA. The programs predicting pseudoknot-free secondary structure of RNA, see [2,3,4,5,6] and review [7], rely on the Nearest Neighbor Model [8, 9]. The tools predicting pseudoknotted secondary structures or three-dimensional (tertiary) structures of RNA [10,11,12,13,14] have significantly lower quality
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