Incorporating Ligands Binding to Specific Sequence/Structure Motifs
Ligand binding to specific hairpin/interior loop like motifs using the Soft Constraints feature.
Typedefs
-
typedef struct vrna_sc_motif_s vrna_sc_motif_t
- #include <ViennaRNA/constraints/ligand.h>
Type definition for soft constraint motif.
Functions
-
int vrna_sc_add_hi_motif(vrna_fold_compound_t *fc, const char *seq, const char *structure, FLT_OR_DBL energy, unsigned int options)
- #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 \(k_d = 0.1 \mu M\), taken from Jenison et al. 1994. At \(1M\) concentration the corresponding binding free energy amounts to \(-9.93~kcal/mol\).
vrna_sc_add_hi_motif(fc, "GAUACCAG&CCCUUGGCAGC", "(...((((&)...)))...)", -9.93, VRNA_OPTION_DEFAULT);
- SWIG Wrapper Notes:
This function is attached as method
sc_add_hi_motif()
to objects of typefold_compound
. The last parameter is optional an defaults tooptions
= VRNA_OPTION_DEFAULT. See, e.g.RNA.fold_compound.sc_add_hi_motif()
in the Python API .
- 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
-
vrna_sc_motif_t *vrna_sc_ligand_detect_motifs(vrna_fold_compound_t *fc, const char *structure)
- #include <ViennaRNA/constraints/ligand.h>
-
vrna_sc_motif_t *vrna_sc_ligand_get_all_motifs(vrna_fold_compound_t *fc)
- #include <ViennaRNA/constraints/ligand.h>
-
struct vrna_sc_motif_s
-
typedef struct vrna_sc_motif_s vrna_sc_motif_t