RNAlib-2.4.16
ligand.h File Reference

Functions for incorporation of ligands binding to hairpin and interior loop motifs using the soft constraints framework. More...

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Data Structures

struct  vrna_sc_motif_s
 

Typedefs

typedef struct vrna_sc_motif_s vrna_sc_motif_t
 

Functions

int vrna_sc_add_hi_motif (vrna_fold_compound_t *vc, const char *seq, const char *structure, FLT_OR_DBL energy, unsigned int options)
 Add soft constraints for hairpin or interior loop binding motif. More...
 

Detailed Description

Functions for incorporation of ligands binding to hairpin and interior loop motifs using the soft constraints framework.

Typedef Documentation

◆ vrna_sc_motif_t

@addtogroup constraints_ligand

@brief  Ligand binding to specific hairpin/interior loop like motifs using the @ref soft_constraints feature

Here is an example that adds a theophylline binding motif. Free energy
contribution is derived from @f$k_d = 0.32 \mu mol / l @f$, taken from
Jenison et al. 1994

@image html   theo_aptamer.svg
@image latex  theo_aptamer.eps

@code{.c}

vrna_sc_add_hi_motif(vc, "GAUACCAG&CCCUUGGCAGC", "(...((((&)...)))...)", -9.22, VRNA_OPTION_DEFAULT);