Table 1. RNA structure prediction accuracy using the RNAStructure (30) Fold algorithm and the SHAPE-Seq v2.0 reactivity data (ρ’s) as constraints, with different m and b parameters.

RNA	Total sensitivity	Total PPV
No SHAPE data	228/360 = 63.3%	229/373 = 61.4%
SHAPE parameters (m = 1.8 and b = −0.6)	292/360 = 81.1%	293/351 = 83.5%
SHAPE-Seq updated parameters (m = 1.1 and b = −0.3)	303/360 = 84.2%	304/342 = 88.9%

Sensitivity and PPV values for each RNA are in Supplementary Tables S4–S6.