title: URS DataBase: universe of RNA structures and their motifs.
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/.
authors.affiliation: Laboratory of Applied Mathematics, Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia Department of Algorithms and Technology of Programming, Faculty of Innovations and High Technology, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region 141700, Russia mroytberg@lpm.org.ru.
authors.forename: Eugene
authors.initials: E
authors.lastname: Baulin
authors.affiliation: Laboratory of Applied Mathematics, Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia Department of Big Data and Information Retrieval, Faculty of Computer Science, National Research University Higher School of Economics, Moscow 101000, Russia.
authors.forename: Victor
authors.initials: V
authors.lastname: Yacovlev
authors.affiliation: Laboratory of Applied Mathematics, Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
authors.forename: Denis
authors.initials: D
authors.lastname: Khachko
authors.affiliation: Department of Mathematical Methods in Biology, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
authors.forename: Sergei
authors.initials: S
authors.lastname: Spirin
authors.affiliation: Laboratory of Applied Mathematics, Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia Department of Algorithms and Technology of Programming, Faculty of Innovations and High Technology, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region 141700, Russia Department of Big Data and Information Retrieval, Faculty of Computer Science, National Research University Higher School of Economics, Moscow 101000, Russia.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Roytberg
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D059372:Nucleotide Motifs / Q000235:genetics*; D012313:RNA / Q000737:chemistry* / Q000235:genetics*
chemical_list: D012313:RNA