URS DataBase: universe of RNA structures and their motifs
| Autor: | Denis Khachko, Eugene Baulin, Mikhail A. Roytberg, Victor Yacovlev, S. A. Spirin |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Structure (mathematical logic) Loop (graph theory) Database Computer science Base pair media_common.quotation_subject Topological classification RNA Computational Biology Nucleotide Motif computer.software_genre General Biochemistry Genetics and Molecular Biology Universe 03 medical and health sciences 030104 developmental biology Databases Genetic Original Article User interface Nucleotide Motifs General Agricultural and Biological Sciences computer Information Systems media_common |
| Zdroj: | Database: The Journal of Biological Databases and Curation |
| ISSN: | 1758-0463 |
| Popis: | 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/. |
| Databáze: | OpenAIRE |
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