Shi-Jie Chen Research Group
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 .
If you wish to access the Vfold web server and package, please visit the Vfold server main page.
 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.
 Cao, S., Chen, S.-J. (2005) Predicting RNA folding thermodynamics with a reduced chain representation model, RNA, 11: 1884-1897.
 Cao, S., Chen, S.-J. (2006) Predicting RNA pseudoknot folding thermodynamics, Nucleic Acids Research, 34: 2634-2652.
 Cao, S., Chen, S.-J. (2009) Predicting structures and stabilities for H-type pseudoknots with interhelix loops, RNA, 15: 696-706.
 Liu, L., Chen, SJ. (2010) Computing the conformational entropy for RNA folds. Journal of Chemical Physics, 132, 235104; doi:10.1063/1.3447385
 Cao, S., Chen, SJ. (2012) A domain-based model for predicting large and complex pseudoknotted structures. RNA Biology. 9: 201-212.
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.
If you wish to access the TBI web server and package, please visit the TBI server main page.
 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.
 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. http://pubs.acs.org/doi/abs/10.1021/jp4010955
 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
 Tan, ZJ., Chen, SJ. (2005) Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte. Journal of Chemical Physics 122, 04490
 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.
. Tan, ZJ., Chen, SJ. (2007) RNA helix stability in mixed Na+/Mg2+ solution. Biophysical Journal 92: 3615-3632.
. Tan, ZJ., Chen, SJ. (2008) Salt dependence of nucleic acid hairpin stability. Biophysical Journal 95: 738-752.
. 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 firstname.lastname@example.org (with cc to email@example.com ).