NAR Molecular Biology Database Collection entry number 283

http://scor.lbl.gov

Tamura, M.¹, Hendrix, D.K.², Klosterman, P.S.¹, Schimmelman, N.R.B.², Brenner, S.E.^1,2, Holbrook, S.R.¹

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

Contact scor@compbio.berkeley.edu

The Structural Classification of RNA (SCOR) is a database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships. SCOR 2.0 provides a survey of the three-dimensional motifs contained in 511 NMR and X-ray RNA structures available as of May 15, 2003. This includes 5,880 secondary structural elements, of which 2,104 are hairpin loops and 3,776 are internal loops. The structural elements are organized in a directed acyclic graph (DAG) architecture, allowing multiple parent classes for a motif. Users can browse the database or search by PDB or NDB identifier, keyword or sequence. Descriptions and cartoon representations of each of the classes are available. RNA motifs reported in the literature (e.g. Kink turns, S-turns, GNRA loops) are incorporated into the classification.

SCOR 2.0 uses a directed acyclic graph (DAG) to represent the relationships among motifs. The DAG allows multiple progenitors to a motif or class. This is necessary for RNA structures, as smaller motifs can be part of larger structural elements, or can be described in more than one way. A new interface has been developed to navigate the DAG-based classification, and a search engine has been added to allow search by PDB identifier, residue number, sequence and keyword. Additionally, 252 new PDB structures were reviewed and their motifs categorized since the previous release, SCOR 1.2. Familiar motifs (e.g., Kink turns, S-turns, GNRA loops) have been added to the classification, and the Ribose Zipper tertiary interaction has been fully classified.

The authors are grateful to the NIGMS of the NIH for support of this project through grant GM 66199 to S.R.H. and S.E.B., and to the NHGRI of the NIH for grant  for grant K22 HG00056 to S.E.B., who is a Searle Scholar.

1. Klosterman, P.S., Tamura, M., Holbrook, S.R., Brenner, S.E. (2002) SCOR: a structural classification of RNA database. Nucleic Acids Res. 30. 392-394.
2. Tamura, M., Holbrook, S.R.  (2002)  Sequence and structural conservation in RNA ribose zippers.  J. Mol. Biol. 320:455-474.
3. Tamura, M., Hendrix, D.K., Klosterman, P.S., Schimmelman, N.R.B., Brenner, S.E. and Holbrook, S.R. (2004)  SCOR: Structural classification of RNA, version 2.0.  Nucleic Acids Res. in press.

Go to the abstract in the NAR 2004 Database Issue.

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