To avoid long computational time, we restrict the sequence length based on the ensemble of conformational space:
(A) <=140 nt for the ensemble of RNA secondary (non-cross linked) structures.
(B) <=110 nt for the ensemble of RNA secondary and H-type pseudoknotted (with inter-helix junction ≤ 1 nt) structures.
(C) <=80 nt for the ensemble of RNA secondary and H-type pseudoknotted (including longer inter-helix junction) structures.
The thermodynamic parameters for base stacks, including mismatched base stacks, are from the Turner parameters (04 version) OR from the MFOLD (2.3 version)
and the loop/junction entropies are from the Vfold model.
References for VfoldThermal:  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. and Chen, S.-J. (2009) Predicting structures and stabilities for H-type pseudoknots with inter-helix loop. RNA, 15, 696-706.
 Cao, S. and Chen, S.-J. (2006) Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Research, 34, 2634-2652;
 Cao, S. and Chen, S.-J. (2005) Predicting RNA folding thermodynamics with a reduced chain representation model. RNA, 11, 1884-1897;
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