Classification of 3D structural character of RNA by hydrogen bond and base stacking.
We are developing a computational system to classify RNA structures by its structural character. Here, an improved grouping algorithm was introduced to the system and the base-stacking pattern (BSP) is used as a criterion for the classification in addition to hydrogen-bond pattern (HBP). 279 conformers of 15 mer RNA hairpin were classified into 89 and 36 groups by HBP and BSP, respectively, suggesting that HBP represents conformational character better than BSP.
Takasu
A
A
Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan.
Watanabe
K
K
Kawai
G
G
D000465:Algorithms; D001483:Base Sequence; D006860:Hydrogen Bonding; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry* / Q000145:classification; D012984:Software
D009843:Oligoribonucleotides; D012313:RNA