Universe of RNA Structures

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Summary

  Universe of RNA Structures (URS) is a web-interface to URS database (URSDB) that includes all RNA-containing PDB entries. The data are annotated; in particular we have pointed out base pairs, stems, loops of various types, pseudoknots, elementary closed regions (ECR), multiplets, etc. For each structural element its specific characteristics are stored. For example, we store pseudoknot signatures and stem-descriptions of ECRs.

  URS allows one
  -  to select a set of PDB entries having desired features;
  -  to obtain statistics for selected subset or for all database;
  -  to analyze the structural elements of the chosen PDB entry.

News

17.09.17 - PDB update (9 entries added).

13.09.17 - DSSR update (up to v1.6.9-2017aug09).

03.09.17 - PDB update (8 entries added).

18.08.17 - PDB update (17 entries added).

03.08.17 - PDB update (20 entries added).

12.07.17 - PDB update (35 entries added).

23.06.17 - PDB update (18 entries added).

09.06.17 - PDB update (21 entries added).

25.05.17 - PDB update (6 entries added).

03.05.17 - PDB update (36 entries added).

21.04.17 - DSSR update (up to v1.6.8-2017mar28).

13.03.17 - PDB update (14 entries added).

25.02.17 - PDB update (10 entries added).

04.02.17 - PDB update (35 entries added).

04.02.17 - DSSR update (up to v1.6.5-2017jan22).

15.01.17 - PDB update (27 entries added).

18.12.16 - PDB update (24 entries added).

04.12.16 - PDB update (24 entries added).

16.11.16 - PDB update (11 entries added).

01.11.16 - PDB update (5 entries added).

25.10.16 - DSSR update (up to v1.6.3-2016oct19).

16.10.16 - PDB update (23 entries added).

03.10.16 - PDB update (17 entries added).

16.09.16 - PDB update (7 entries added).

05.09.16 - PDB update (5 entries added).

22.08.16 - PDB update (22 entries added).

22.08.16 - DSSR update (up to v1.6.0-2016aug06).

28.07.16 - PDB update (17 entries added).

08.07.16 - PDB update (11 entries added).

24.06.16 - PDB update (13 entries added).

16.06.16 - DSSR update (up to v1.5.6-2016jun09).

09.06.16 - PDB update (32 entries added).

18.05.16 - PDB update (8 entries added).

04.05.16 - PDB update (31 entries added).

20.04.16 - PDB update (14 entries added).

15.04.16 - DSSR update (up to v1.5.3-2016apr11).

06.04.16 - PDB update (18 entries added).

19.03.16 - PDB update (7 entries added).

04.03.16 - PDB update (10 entries added).

19.02.16 - PDB update (3 entries added).

05.02.16 - PDB update (23 entries added).

01.02.16 - DSSR update (up to v1.4.9-2016jan25).

22.01.16 - PDB update (34 entries added).

21.01.16 - DSSR update (up to v1.4.7-2016jan06).

18.12.15 - PDB update (7 entries added).

04.12.15 - PDB update (14 entries added).

13.11.15 - PDB update (11 entries added).

07.11.15 - DSSR update (up to v1.4.3-2015oct23).

30.10.15 - PDB update (32 entries added).

03.10.15 - DSSR update (up to v1.3.8-2015oct02).

01.10.15 - PDB update (23 entries added).

17.09.15 - PDB update (14 entries added).

02.09.15 - PDB update (37 entries added).

03.08.15 - PDB update (49 entries added).

25.05.15 - switched to mmCIF format (2812 entries in total).

10.12.14 - PDB update (6 entries added).

25.11.14 - PDB update (17 entries added).

05.11.14 - PDB update (107 entries added).

08.10.14 - PDB update (16 entries added).

18.09.14 - PDB update (18 entries added).

03.09.14 - PDB update (33 entries added).

13.08.14 - PDB update (54 entries added).

30.07.14 - PDB update (46 entries added).

16.07.14 - PDB update (17 entries added).

02.07.14 - PDB update (15 entries added).

18.06.14 - PDB update (77 entries added).

Structures

  To select the desired set of structures one can use a wide range of parameters related to general information about the entries, macromolecular content, RNA structure patterns and RNA interactions. To form a search query one have to use the advanced search of the Structures page. It allows one to formulate a query as a disjunction (OR-junction) of conjunctions (AND-junctions) of elementary queries; the number of items in a conjunction can be arbitrary large. The user can edit previous queries, perform search in previous search results or add the new results to the results of the previous search.

Statistics

  URS allows users to view statistics related to chains, base pairs, links, stems, loops, pseudoknots, multiplets and RNA-protein H-bonds.

  The request may be carried out in three modes: for the entire database, for the selected set of structures and for a selected PDB entry.

  Currently URSDB contains 3614 PDB entries, 9776 RNA Chains, 1837838 Base Pairs and 6068 Pseudoknots.