Estimating RNA Loop Entropies Using a New Nucleobase Model and Sequential Monte Carlo Method  

作　　者：LIN Hui ZHANG Jian 林辉;张建(School of Business,Nanjing University,Nanjing 210093;National Laboratory of Solid State Microstructure,Department of Physics,Nanjing University,Nanjing 210093)

机构地区：[1]School of Business,Nanjing University,Nanjing 210093 [2]National Laboratory of Solid State Microstructure,Department of Physics,Nanjing University,Nanjing 210093

出　　处：《Chinese Physics Letters》2011年第8期336-339,共4页中国物理快报（英文版）

基　　金：by the National Natural Science Foundation of China under Grant No 10974088.

摘　　要：We report a new scheme that is designed to accurately and efficiently compute the entropy of RNA loops.The scheme is based on a new RNA nucleobase discrete state(RNAnbds)model and a Sequential Monte Carlo(SMC)method.The novelty of the RNAnbds model is that it directly represents the conformation of the RNA nucleobases,instead of the RNA backbones.To test the performance of this new scheme,we calculate the entropies for RNA hairpin loops and compare the results with the exact computational values obtained by an enumeration strategy and with the experimental data.It is found that the SMC method gives almost indistinguishable results from enumerations for short loops.For long hairpin loops,it also provides a good estimation that agrees with experiments.

关 键 词：base scheme BACKBONE 

分 类 号：TN9[电子电信—信息与通信工程]