PMC:1459172 / 19439-20200 JSONTXT

{"project":"2_test","denotations":[{"id":"16722605-1695107-1692562","span":{"begin":23,"end":25},"obj":"1695107"}],"text":"McCaskill's algorithm [31] computes the base pairing probabilities from the partition functions of subsequences. Again, it seems easier to first perform the backtracking recursions on the \"raw\" partition functions that do not take into account the initiation contribution. This yields pairing probabilities Pkl for an ensemble of structures that does not distinguish between true dimers and isolated structures for A and B and ignores the initiation energy. McCaskill's backwards recursions are formally almost identical to the case of folding a single linear sequence. We only have to exclude multiloop contributions in which the cut-point u between components coincides with the cut point c. All other cases are already taken care of in the forward recursion."}