PMC:1459172 / 31393-32531 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1459172","sourcedb":"PMC","sourceid":"1459172","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1459172","text":"Limitations and future extensions\nWe have described here an algorithm to compute the partition function of the secondary structure of RNA dimers and to model in detail the thermodynamics of a mixture of two RNA species. At present, RNAcofold implements the most sophisticated method for modeling the interactions of two (large) RNAs. Because the no-pseudoknot condition is enforced to limit computational costs, our approach disregards certain interaction structures that are known to be important, including kissing hairpin complexes.\nThe second limitation, which is of potential importance in particular in histochemical applications, is the restriction to dimeric complexes. More complex oligomers are likely to form in reality. The generalization of the present approach to trimers or tetramers is complicated by the fact that for more than two molecules the results of the calculation are not independent of the order of the concatenation any more, so that for M-mers (M - 1)! permutations have to be considered separately. This also leads to bookkeeping problems since every secondary structure still has to be counted exactly once.","divisions":[{"label":"title","span":{"begin":0,"end":33}},{"label":"p","span":{"begin":34,"end":535}}],"tracks":[]}