Ligand binding to specific hairpin/interior loop like motifs using the Soft Constraints feature.
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Ligand binding to specific hairpin/interior loop like motifs using the Soft Constraints feature.
typedef struct vrna_sc_motif_s vrna_sc_motif_t
Type definition for soft constraint motif.
◆ vrna_sc_motif_s
◆ vrna_sc_add_hi_motif()
#include <ViennaRNA/constraints/ligand.h >
Add soft constraints for hairpin or interior loop binding motif.
Here is an example that adds a theophylline binding motif. Free energy contribution is derived from , taken from Jenison et al. 1994. At concentration the corresponding binding free energy amounts to .
"GAUACCAG&CCCUUGGCAGC" ,
"(...((((&)...)))...)" ,
int vrna_sc_add_hi_motif(vrna_fold_compound_t *fc, const char *seq, const char *structure, FLT_OR_DBL energy, unsigned int options)
Add soft constraints for hairpin or interior loop binding motif.
#define VRNA_OPTION_DEFAULT
Option flag to specify default settings/requirements.
Definition: fold_compound.h:375
Parameters
fc The vrna_fold_compound_t the motif is applied to
seq The sequence motif (may be interspaced by '&' character
structure The structure motif (may be interspaced by '&' character
energy The free energy of the motif (e.g. binding free energy)
options Options
Returns non-zero value if application of the motif using soft constraints was successful
SWIG Wrapper Notes: This function is attached as method sc_add_hi_motif() to objects of type fold_compound