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. Author manuscript; available in PMC: 2016 Jun 1.
Published in final edited form as: Methods. 2015 Feb 14;0:60–66. doi: 10.1016/j.ymeth.2015.02.003

Table 2.

Methods for RNA tertiary structure prediction discussed in this review.

Method Name Probing Protocol Computational
Method		 Strategy
Sequence-encoded cleavage [110] HRP + SHAPE DMD Place Fe(II)-EDTA at specific nucleotides and find their neighbors by using HRP.
iFoldRNA-HRP [119] HRP DMD Convert the HRP reactivities into the numbers of neighbors and use them as the constraints.
RING-MaP [120] SHAPE-MaP DMD Model the correlation among the reactive sites in one RNA strand as through-space interaction.
MOCHA [122] HRP FARNA Generate 2D mapping between interacted nucleotides by performing HRP on RNAs randomly.
MS3D [124, 125] Bifunctional crosslinking MC-Sym Detect spatially conjugated nucleotides by using mass mapping technique.