I'm interested in the 3D structure of RNA molecules such as in the case of tRNA. So I need a tool which can predict the 3D structure given the sequence of the transcript.
The Assemble package is made for you:
http://bioinformatics.org/assemble/
Cheers,
Claude
If you happen to have experimentally determined secondary structure of your RNA (e.g via chemical probing or SHAPE), you might find RNAComposer to be a quite useful tool. See the following website: http://rnacomposer.cs.put.poznan.pl/Home
Hi, there are many models including knowledge-based and physics-based can be used to predict RNA 3D structures. More details can be found in the following reviiew and papers:
Ya-Zhou Shi, Yuan-Yan Wu, Feng-Hua Wang, Zhi-Jie Tan*, RNA structure prediction: Progress and perspective. Chinese Physics B. 23(7) 078701, 2014.
Ya-Zhou Shi, Feng-Hua Wang, Yuan-Yan Wu, Zhi-Jie Tan*, A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect. The Journal of Chemical Physics; 141(10) 105102, 2014.
Ya-Zhou Shi, Lei Jin, Feng-Hua Wang, Xiao-Long Zhu, and Zhi-Jie Tan*, Predicting 3D structure, flexibility and stability of RNA hairpins in monovalent and divalent ion solutions. Biophysical Journal 109: 2654-2665, 2015.
Best wishes
https://www.researchgate.net/profile/Ya_Zhou_Shi
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