The types of various structure that can be modeled by a PCFG include long range interactions, pairwise structure and other nested structures. However, pseudoknots can not be modeled. PCFGs extend CFG by assigning probabilities to each production rule. A maximum probability parse tree from the grammar implies a maximum probability structure. Since RNAs preserve their structures over their primary sequence; RNA structure prediction can be guided by combining evolutionary information from comparative sequence analysis with biophysical knowledge about a structure plausibility based on such probabilities. Also search results for structural homologs using PCFG rules are scored according to PCFG derivations probabilities. Therefore, building grammar to model the behavior of base-pairs and single-stranded regions starts with exploring features of structural multiple sequence alignment of related RNAs.