To avoid long computational time, we restrict the sequence length based on the ensemble of conformational space:
(1) <=600 nt for the ensemble of RNA secondary (non-cross linked) structures.
(2) <=150 nt for the ensemble of RNA H-type pseudoknotted structures, besides (1).
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 Vfold2D:  Cheng Y, Zhang S, Xu X, Chen SJ. Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding. The Journal of Physical Chemistry B. 2021 Sep 2;125(36):10108-18.
 Xu, XJ., Chen, SJ. (2016) A method to predict the structure and stability of RNA/RNA complexes. Methods Mol Biol. 1490:63-72. doi: 10.1007/978-1-4939-6433-8_5.
 Xu, XJ., Chen, SJ. (2015) Modeling the structure of RNA scaffold. Methods Mol Biol. 1316: 1-11. doi: 10.1007/978-1-4939-2730-2_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.
 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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