Classification of RNA structures based on hydrogen bond and base-base stacking patterns: application for NMR structures.
A computational system, CSNA, for classifying RNA structures according to structural characters was developed. CSNA lists up all the hydrogen bonds and base-base stackings in the structures, and classifies the structures into sub-groups based on their patterns as the first step grouping. The frequency of each hydrogen bond or base-base stacking is calculated, the frequency score being defined as the sum of the frequency of existing hydrogen bonds or base-base stackings for each sub-group. Finally, the sub-groups are further classified into groups based on the frequency score defined in this study and the difference between the patterns. According to the frequency score, CSNA suggests a group that shares most frequently appearing hydrogen bonds and base-base stackings. CSNA was applied to the classification of the results of two individual simulated annealing calculations based on NMR information. It was found that CSNA could extract structures with lower energy without checking any energy term and could provide well converged groups as the lowest energy structures. Thus, CSNA could be a new tool for structural determination of nucleic acids.
Takasu
Akitsugu
A
Department of Industrial Chemistry, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba 275-0016, Japan.
Watanabe
Kimitsuna
K
Kawai
Gota
G
D000465:Algorithms; D000818:Animals; D020029:Base Pairing; D006801:Humans; D006860:Hydrogen Bonding; D008956:Models, Chemical; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D013768:Tetrahymena / Q000235:genetics
D012313:RNA