Shi-Jie Chen Research Group








Vfold model

Vfold [1-6] is a software package to evaluate the stable structures and the folding free energies for RNA secondary structures and pseudoknotted structures. Recently, the Vfold model has been extended to predict loop-stem tertiary interactions in RNA pseudoknots [6].

If you wish to access the Vfold web server and package, please visit the Vfold server main page.

[1] Xu, XJ., Zhao, PN., Chen, SJ. (2014) Vfold: a web server for RNA structure and folding thermodynamics prediction. PLoS ONE doi: 10.1371/journal.pone.0107504.

[2] Cao, S., Chen, S.-J. (2005) Predicting RNA folding thermodynamics with a reduced chain representation model, RNA, 11: 1884-1897.

[3] Cao, S., Chen, S.-J. (2006) Predicting RNA pseudoknot folding thermodynamics, Nucleic Acids Research, 34: 2634-2652.

[4] Cao, S., Chen, S.-J. (2009) Predicting structures and stabilities for H-type pseudoknots with interhelix loops, RNA, 15: 696-706.

[5] Liu, L., Chen, SJ. (2010) Computing the conformational entropy for RNA folds. Journal of Chemical Physics, 132, 235104; doi:10.1063/1.3447385

[6] Cao, S., Chen, SJ. (2012) A domain-based model for predicting large and complex pseudoknotted structures. RNA Biology. 9: 201-212.

TBI model

Tightly Bound Ion (TBI) [7-14] is a software package to evaluate the ion-dependent folding stability for nucleic acids.

If you wish to access the TBI web server and package, please visit the TBI server main page.

[7] Zhu, YH, He, ZJ., Chen, SJ. (2015) TBI server: a web server for predicting ion effects in RNA folding. PLoS ONE doi: 10.1371/journal.pone.0119705.

[8] He, ZJ., Chen, SJ. (2013) Quantifying Coulombic and Solvent Polarization-Mediated Forces Between DNA Helices. J. Phys. Chem. B, 117 (24), pp 7221-7227. DOI: 10.1021/jp4010955.

[9] He, ZJ., Chen, SJ. (2012) Predicting ion-nucleic acid interactions by energy landscape-guided sampling. Journal of Chemical Theory and Computation, 8 (6), pp 2095-2102. DOI: 10.1021/ct300227a

[10] Tan, ZJ., Chen, SJ. (2005) Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte. Journal of Chemical Physics 122, 04490

[11] Tan, ZJ., Chen, SJ. (2006) Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophysical Journal 90: 1175-1190.

[12]. Tan, ZJ., Chen, SJ. (2007) RNA helix stability in mixed Na+/Mg2+ solution. Biophysical Journal 92: 3615-3632.

[13]. Tan, ZJ., Chen, SJ. (2008) Salt dependence of nucleic acid hairpin stability. Biophysical Journal 95: 738-752.

[14]. Tan, ZJ, Chen, SJ. (2011) Salt contribution to RNA tertiary structure folding stability. Biophysical Journal, 101: 176-187.

Please address all questions and comments about the Vfold and TBI softwares to (with cc to ).