A method for finding optimal rna secondary structures using a new entropy model (vsfold).
We are developing a program to calculate optimal RNA secondary structures. The model uses di-nucleotide pairing energies as with most traditional approaches. However, for long-range entropy interactions, the approach uses an entropy-loss model based on the accumulated sum of the entropy of bonding between each base-pair weighted inversely by the correlation of the RNA sequence (the Kuhn length). Stiff RNA forms very different structures from flexible RNA. The results demonstrate that the long-range folding is largely governed by this entropy and the Kuhn length.
Dawson
Wayne
W
Department of Life and Environmental Sciences, Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan. wayne.dawson@it-chiba.ac.jp
Fujiwara
Kazuya
K
Kawai
Gota
G
Futamura
Yasuhiro
Y
Yamamoto
Kenji
K
D019277:Entropy; D008956:Models, Chemical; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
D012313:RNA