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Nucleic Acids Research, 2003, Vol. 31, No. 16 4755-4761
© 2003 Oxford University Press

RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space

Carlos M. Duarte, Leven M. Wadley1 and Anna Marie Pyle*,2,3

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA, 1 Department of Physics, Columbia University, New York, NY 10027, USA, 2 Department of Molecular Biophysics and Biochemistry and 3 Howard Hughes Medical Institute, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA

*To whom correspondence should be addressed. Tel: +1 203 432 5633; Fax: +1 203 432 5316; Email: anna.pyle{at}yale.edu

Given the wealth of new RNA structures and the growing list of RNA functions in biology, it is of great interest to understand the repertoire of RNA folding motifs. The ability to identify new and known motifs within novel RNA structures, to compare tertiary structures with one another and to quantify the characteristics of a given RNA motif are major goals in the field of RNA research; however, there are few systematic ways to address these issues. Using a novel approach for visualizing and mathematically describing macromolecular structures, we have developed a means to quantitatively describe RNA molecules in order to rapidly analyze, compare and explore their features. This approach builds on the alternative {eta},{theta} convention for describing RNA torsion angles and is executed using a new program called PRIMOS. Applying this methodology, we have successfully identified major regions of conformational change in the 50S and 30S ribosomal subunits, we have developed a means to search the database of RNA structures for the prevalence of known motifs and we have classified and identified new motifs. These applications illustrate the powerful capabilities of our new RNA structural convention, and they suggest future adaptations with important implications for bioinformatics and structural genomics.


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