Partition Function Cofolding as stepwise process. More...
|pu_contrib *||pf_unstru (char *sequence, int max_w)|
|Calculate the partition function over all unpaired regions of a maximal length. |
|interact *||pf_interact (const char *s1, const char *s2, pu_contrib *p_c, pu_contrib *p_c2, int max_w, char *cstruc, int incr3, int incr5)|
|Calculates the probability of a local interaction between two sequences. |
|void||free_interact (interact *pin)|
|Frees the output of function pf_interact(). |
|void||free_pu_contrib_struct (pu_contrib *pu)|
|Frees the output of function pf_unstru(). |
Partition Function Cofolding as stepwise process.
In this approach to cofolding the interaction between two RNA molecules is seen as a stepwise process. In a first step, the target molecule has to adopt a structure in which a binding site is accessible. In a second step, the ligand molecule will hybridize with a region accessible to an interaction. Consequently the algorithm is designed as a two step process: The first step is the calculation of the probability that a region within the target is unpaired, or equivalently, the calculation of the free energy needed to expose a region. In the second step we compute the free energy of an interaction for every possible binding site.