Statistical analysis of RNA backbone.
Local conformation is an important determinant of RNA catalysis and binding. The analysis of RNA conformation is particularly difficult due to the large number of degrees of freedom (torsion angles) per residue. Proteins, by comparison, have many fewer degrees of freedom per residue. In this work, we use and extend classical tools from statistics and signal processing to search for clusters in RNA conformational space. Results are reported both for scalar analysis, where each torsion angle is separately studied, and for vectorial analysis, where several angles are simultaneously clustered. Adapting techniques from vector quantization and clustering to the RNA structure, we find torsion angle clusters and RNA conformational motifs. We validate the technique using well-known conformational motifs, showing that the simultaneous study of the total torsion angle space leads to results consistent with known motifs reported in the literature and also to the finding of new ones.
Hershkovitz
Eli
E
Schools of Electrical and Computer Engineering and Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0250, USA. eli@theor.chemistry.gatech.edu
Sapiro
Guillermo
G
Tannenbaum
Allen
A
Williams
Loren Dean
LD
D001483:Base Sequence; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure*; D017423:Sequence Analysis, RNA / Q000379:methods*
D012313:RNA