| CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY |
|
|
|
|
Estimating RNA Loop Entropies Using a New Nucleobase Model and Sequential Monte Carlo Method |
| LIN Hui**, ZHANG Jian**
|
1School of Business, Nanjing University, Nanjing 210093
2National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093
|
|
| Cite this article: |
|
LIN Hui, ZHANG Jian 2011 Chin. Phys. Lett. 28 088702 |
|
|
|
|
Abstract 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.
|
| Keywords:
87.14.Gk
87.15.Bg
87.64.Aa
|
|
|
Received: 10 May 2011
Published: 28 July 2011
|
|
|
|
|
|
|
|
[1] Gesteland R F, Cech T R and Atkins J F 2006 The RNA World 3rd edn (New York: Cold Spring Harbor Press) chapt 11
[2] Mathews D H et al 1999 J. Mol. Biol. 288 911
[3] Serra M J and Turner D H 1995 Methods in Enzymology 259 242
[4] Xia T et al 1998 Biochemistry 37 14719
[5] Mathews D H and Turner D H 2002 Biochemistry 41 869
[6] McCaskill J S 1990 Biopolymers 29 1105
[7] Chen S J and Dill K A 1995 J. Chem. Phys. 103 5802
[8] Chen S J and Dill K A 1998 J. Chem. Phys. 109 4602
[9] Chen S J and Dill K A 2000 Proc. Natl. Acad. Sci. 97 646
[10] Zhang W and Chen S J 2001 J. Chem. Phys. 114 7669
[11] Cao S and Chen S J 2005 RNA 11 1884
[12] Liang J 2002 J. Chem. Phys. 117 3511
[13] Zhang J F et al 2004 J. Chem. Phys. 121 592
[14] Zhang J F 2007 Proteins 66 61
[15] Zhang J, Zhang Y J and Wang W 2010 Chin. Phys. Lett. 27 118702
[16] Zhang J et al 2009 RNA 15 2248
[17] Murray L J W et al 2003 Proc. Natl. Acad. Sci. USA 100 13904
[18] Das R and Baker D 2007 Proc. Natl. Acad. Sci. USA 104 14664
[19] Fearnhead P and Clifford P 2003 J. R. Stat. Soc. B 65 887
[20] Park B and Levitt M 1995 J. Mol. Biol. 249 493
[21] Zhang J F et al 2006 Proteins 63 949
[22] Jacobson H and Stockmayer W H 1950 J. Chem. Phys. 18 1600
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
