RNAlib-2.5.1
Incorporating Ligands Binding to Specific Sequence/Structure Motifs using Soft Constraints

Ligand binding to specific hairpin/interior loop like motifs using the Soft Constraints feature. More...

Detailed Description

Ligand binding to specific hairpin/interior loop like motifs using the Soft Constraints feature.

+ Collaboration diagram for Incorporating Ligands Binding to Specific Sequence/Structure Motifs using Soft Constraints:

Data Structures

struct  vrna_sc_motif_s
 

Typedefs

typedef struct vrna_sc_motif_s vrna_sc_motif_t
 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)
 Add soft constraints for hairpin or interior loop binding motif. More...
 

Data Structure Documentation

◆ vrna_sc_motif_s

struct vrna_sc_motif_s

Function Documentation

◆ vrna_sc_add_hi_motif()

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 $-9.93~kcal/mol$.

"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
fcThe vrna_fold_compound_t the motif is applied to
seqThe sequence motif (may be interspaced by '&' character
structureThe structure motif (may be interspaced by '&' character
energyThe free energy of the motif (e.g. binding free energy)
optionsOptions
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