Local Stability Compensation

bpRNA_data contains tab-delimited files for bulges, hairpin loops, and internal loops in bpRNA-1 and contains a list of the structures that are a part of bpRNA-1m90, which may be used to filter the structures down to a subset with < 90% sequence identity. The tab-delimited text files contain information (including calculated thermodynamic values) about each instance of a bulge, hairpin, and internal loop in bpRNA-1m as well as information about the stems adjacent to the each loop. Within the directory 'refold' is a similar set of .txt files containing information on bulges, hairpins, and internal loops after folding CRW and RFAM structures using existing pairs as a constraint.
library_data contains DMS reactivity data in the form of the original filtered sequence libraries used in the study in .csv format, as well as structure type energy (.ste) files for both the library sequences as designed and the library sequences as folded according to ViennaRNA's RNAfold. Lastly, the .txt files contain processed tab-delimited data collected for each sequence in each library, including free energies, average reactivities, and area under the receiver operator curve (AUROC) values for different localities.