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Nucleic Acids Research, 2004, Vol. 32, Database issue D182-D184
© 2004 Oxford University Press

SCOR: Structural Classification of RNA, version 2.0

Makio Tamura1, Donna K. Hendrix2, Peter S. Klosterman1,2, Nancy R. B. Schimmelman2, Steven E. Brenner1,2 and Stephen R. Holbrook*,1

1 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and 2 Department of Plant and Microbial Biology, 111 Koshland Hall #3102, University of California, Berkeley, CA 94720-3102, USA

*To whom correspondence should be addressed at Department of Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 64–123, Berkeley, CA 94720, USA. Tel: +1 510 486 4304; Fax: +1 510 486 6059; Email: srholbrook{at}lbl.gov

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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