Small nucleolar RNAs are an abundant class of non-coding RNAs that guide chemical modifications of rRNAs, snRNAs and some mRNAs. In the case of many orphan snoRNAs, the targeted nucleotides remain unknown, however. The box H/ACA subclass determines uridine residues that are to be converted into pseudouridines via specific complementary binding in a well-defined secondary structure configuration that is outside the scope of common RNA (co-)folding algorithms.