SCOR: Structural Classification of RNA, Version 2.0

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2003 Dec 19

PMID 14681389

Citations 56

Authors

Makio Tamura

Donna K Hendrix

Peter S Klosterman

Nancy R B Schimmelman

Steven E Brenner

Stephen R Holbrook

Affiliations

Soon will be listed here.

Abstract

SCOR, the Structural Classification of RNA (http://scor.lbl.gov), is a database designed to provide a comprehensive perspective and understanding of RNA motif three-dimensional structure, function, tertiary interactions and their relationships. SCOR 2.0 represents a major expansion and introduces a new classification organization. The new version represents the classification as a Directed Acyclic Graph (DAG), which allows a classification node to have multiple parents, in contrast to the strictly hierarchical classification used in SCOR 1.2. SCOR 2.0 supports three types of query terms in the updated search engine: PDB or NDB identifier, nucleotide sequence and keyword. We also provide parseable XML files for all information. This new release contains 511 RNA entries from the PDB as of 15 May 2003. A total of 5880 secondary structural elements are classified: 2104 hairpin loops and 3776 internal loops. RNA motifs reported in the literature, such as 'Kink turn' and 'GNRA loops', are now incorporated into the structural classification along with definitions and descriptions.

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References

Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H . The Protein Data Bank. Nucleic Acids Res. 1999; 28(1):235-42. PMC: 102472. DOI: 10.1093/nar/28.1.235. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Wimberly B, Brodersen D, Clemons Jr W, Morgan-Warren R, Carter A, Vonrhein C . Structure of the 30S ribosomal subunit. Nature. 2000; 407(6802):327-39. DOI: 10.1038/35030006. View

Klinck R, Westhof E, Walker S, Afshar M, Collier A . A potential RNA drug target in the hepatitis C virus internal ribosomal entry site. RNA. 2000; 6(10):1423-31. PMC: 1370013. DOI: 10.1017/s1355838200000935. View

Gendron P, Lemieux S, Major F . Quantitative analysis of nucleic acid three-dimensional structures. J Mol Biol. 2001; 308(5):919-36. DOI: 10.1006/jmbi.2001.4626. View

Klein D, Schmeing T, Moore P, Steitz T . The kink-turn: a new RNA secondary structure motif. EMBO J. 2001; 20(15):4214-21. PMC: 149158. DOI: 10.1093/emboj/20.15.4214. View

Klosterman P, Tamura M, Holbrook S, Brenner S . SCOR: a Structural Classification of RNA database. Nucleic Acids Res. 2001; 30(1):392-4. PMC: 99131. DOI: 10.1093/nar/30.1.392. View

Tamura M, Holbrook S . Sequence and structural conservation in RNA ribose zippers. J Mol Biol. 2002; 320(3):455-74. DOI: 10.1016/s0022-2836(02)00515-6. View

Holbrook S, Sussman J, Warrant R, Kim S . Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. J Mol Biol. 1978; 123(4):631-60. DOI: 10.1016/0022-2836(78)90210-3. View

10.

Heus H, Pardi A . Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science. 1991; 253(5016):191-4. DOI: 10.1126/science.1712983. View

11.

Berman H, Olson W, Beveridge D, Westbrook J, Gelbin A, Demeny T . The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J. 1992; 63(3):751-9. PMC: 1262208. DOI: 10.1016/S0006-3495(92)81649-1. View

12.

Szewczak A, Moore P . The sarcin/ricin loop, a modular RNA. J Mol Biol. 1995; 247(1):81-98. DOI: 10.1006/jmbi.1994.0124. View

13.

Jucker F, Pardi A . GNRA tetraloops make a U-turn. RNA. 1995; 1(2):219-22. PMC: 1369075. View

14.

Guex N, Peitsch M . SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1998; 18(15):2714-23. DOI: 10.1002/elps.1150181505. View

15.

Legault P, Li J, Mogridge J, Kay L, GREENBLATT J . NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell. 1998; 93(2):289-99. DOI: 10.1016/s0092-8674(00)81579-2. View

16.

Leontis N, Westhof E . A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs. J Mol Biol. 1998; 283(3):571-83. DOI: 10.1006/jmbi.1998.2106. View

17.

Duarte C, Pyle A . Stepping through an RNA structure: A novel approach to conformational analysis. J Mol Biol. 1999; 284(5):1465-78. DOI: 10.1006/jmbi.1998.2233. View