Vfold2D (version 2.0): Predicting RNA 2D structures
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References for Vfold2D:
[1] 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.
[2] 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.
[3] 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.
[4] 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.
[5] Cao, S. and Chen, S.-J. (2009) Predicting structures and stabilities for H-type pseudoknots with inter-helix loop. RNA, 15, 696-706.
[6] Cao, S. and Chen, S.-J. (2006) Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Research, 34, 2634-2652;
[7] 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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